Two new cyano-bridged bimetallic complexes, [Cu(TAAB)Fe(CN) 5(NO)]·2H 2O ( 1) and [Mn(bpy) 2(H 2O)Fe(CN) 5(NO)]·H 2O ( 2) (where TAAB = tetrabenzo[ b, f, j, n][1,5,9,l3]tetraaza-cyclohexadecine and bpy = 2,2'-bipyridine), have been synthesized and characterized by elemental analyses, IR spectra and TG-DSC analyses. Single crystal X-ray structure analyses revealed that the complex 1 has a cyano-bridged binuclear structure in which Cu(II) center is coordinated by tetraazacyclic TAAB ligand to form an intriguing saddle-shaped structure, and Fe(II) center is in an octahedral coordination environment with nitrosyl group trans to the cyano-bridge. In complex 2, Mn(II) center is cis six-coordinated and linked to nitroprusside though a bridging cyanide group to form a binuclear structure, while the nitrosyl group is cis to the cyano-bridge. The thermal stabilities of both complexes were investigated, which shows the nitrosyl and cyanide groups of nitroprusside released by two-steps in the temperature range of 200-380 °C.

Quantum chemistry calculations of CASSCF/CASPT2 level together with ligand field analysis are used for the investigation of magnetic anisotropy of [Mo(CN)7]4- complexes. We have considered three types of heptacyano environments: two ideal geometries, a pentagonal bipyramid and a capped trigonal prism, and the heptacyanomolybdate fragment of the cyano-bridged magnetic network K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O. At all geometries the first excited Kramers doublet is found remarkably close to the ground one due to a small orbital energy gap in the ligand field spectrum, which ranges between a maximal value in the capped trigonal prism (800 cm(-1)) and zero in the pentagonal bipyramid. The small value of this gap explains (i) the axial form of the g tensor and (ii) the strong magnetic anisotropy even in strongly distorted complexes. Comparison with available experimental data for the g tensor of the mononuclear precursors reveals good agreement with the present calculations for the capped trigonal prismatic complex and a significant discrepancy for the pentagonal bipyramidal one. The calculations for the heptacyanomolybdate fragment of K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O give g(perpendicular)/g(parallel) approximately 0.5 and the orientation of the local anisotropy axis close to the symmetry axis of an idealized pentagonal bipyramid. These findings are expected to be important for the understanding of the magnetism of anisotropic Mo(III)-Mn(II) cyano-bridged networks based on the [Mo(CN)7]4- building block. PMID:16834090

Prussian blue (PB) nanoparticles, one of many cyano-bridged coordination polymers, are successfully incorporated into chitosan (CS) polymer to prepare PB/CS mixed matrix membranes (MMMs). The PB nanoparticles are uniformly distributed in the MMMs without the collapse of the original PB structure. As-prepared PB/CS MMMs are used for ethanol dehydration at 25 °C in the pervaporation process. The effect of loading PB in CS matrix on pervaporation performance is carefully investigated. The PB/CS membrane with 30 wt% PB loading shows the best performance with a permeate flux of 614 g. m-2 . h-1 and a separation factor of 1472. The pervaporation using our PB/CS membranes exhibits outstanding performance in comparison with the previously reported CS-based membranes and MMMs. Furthermore, the addition of PB allows PB/CS MMMs to be tolerant of acidic environment. The present work demonstrates good pervaporation performance of PB/CS MMMs for the separation of an ethanol/water (90:10 in wt%) solution. Our new system provides an opportunity for dehydration of bioethanol in the future. PMID:27451778

Three cyanobridged hetero-metallic complexes of general formula, [Cu(NH3)2(μ-ampy)M(μ-CN)2(CN)2]n [ampy=4-aminomethylpyridine, M=Ni(II) (1), Pd(II) (2) and Pt(II) (3)] have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal analyses and elemental analyses. The complexes crystallize in triclinic system with space group P-1. In all complexes, M(II) ions are coordinated by four cyano ligands, and four N atoms in the equatorial plane around the Cu atom form a slightly distorted square-planar arrangement, while the slightly distorted octahedral coordination is completed by the cyanide N atoms in the axial positions. In one-dimensional structures of all the complexes, [Cu(ampy)](2+) cations and [M(CN)4](2-) anions are linked via bridging cyano ligands. The adjacent one-dimensional structures form a 2D network to connect by the μ-ampy bridging ligands. The 2D layers are further linked by metal⋯π and hydrogen bonding interactions to generate a three dimensional network. PMID:24239763

Cyano-bridged Gd(3+)/[Fe(CN)6](3-) coordination polymer nanoparticles of 3-4 nm stabilized with D-mannitol presenting a high r1 relaxivity value of 11.4 mM(-1) s(-1) were investigated in vivo as contrast agents (CA) for Magnetic Resonance Imaging (MRI). They allow an increase of the MR image contrast and can act as an efficient intravascular T1 CA with a relatively long blood-circulation lifetime (60 min) without specific toxicity. PMID:25967733

The cyanobridged complex of triethylenetetramine was characterized by FT-IR, Raman spectroscopy and X-ray single crystal diffraction analysis. The molecular geometry and vibrational frequencies of the complex in the ground state have been calculated by using B3LYP density functional method with LANL2DZ basis set. A good correlation was found via comparison of the experimental and theoretical vibrational frequencies of complex. The complex of the type [Zn(teta)Ni(μ-CN)2(CN)2]n has been studied in the 4000-250 cm-1 region and assignment of all the observed bands were made. The analysis of the FT-IR and Raman spectra indicates that there are some structure spectra correlations.

Photocatalytic hydroxylation of benzene to phenol was achieved by using O2 as an oxidant as well as an oxygen source with a cyano-bridged polynuclear metal complex containing Fe(II) and Ru(II) incorporated in mesoporous silica-alumina ([Fe(H2O)3]2[Ru(CN)6]@sAl-MCM-41). An apparent turnover number (TON) of phenol production per the monomer unit of [Fe(H2O)3]2[Ru(CN)6] was 41 for 59 h. The cyano-bridged polynuclear metal complex, [Fe(H2O)3]2[Ru(CN)6], exhibited catalytic activity for thermal hydroxylation of benzene by H2O2 in acetonitrile (MeCN), where the apparent TON of phenol production reached 393 for 60 h. The apparent TON increased to 2500 for 114 h by incorporating [Fe(H2O)3]2[Ru(CN)6] in sAl-MCM-41. Additionally, [Fe(H2O)3]2[Ru(CN)6] acts as a water oxidation catalyst by using [Ru(bpy)3](2+) (bpy = 2,2'-bipyridine) and Na2S2O8 as a photosensitizer and a sacrificial electron acceptor as evidenced by (18)O-isotope labeling experiments. Photoirradiation of an O2-saturated MeCN solution containing [Fe(H2O)3]2[Ru(CN)6]@sAl-MCM-41 and scandium ion provided H2O2 formation, where photoexcited [Ru(CN)6](4-) moiety reduces O2 as indicated by laser flash photolysis measurements. Thus, hydroxylation of benzene to phenol using molecular oxygen photocatalyzed by [Fe(H2O)3]2[Ru(CN)6] occurred via a two-step route; (1) molecular oxygen was photocatalytically reduced to peroxide by using water as an electron donor, and then (2) peroxide thus formed is used as an oxidant for hydroxylation of benzene. PMID:27265780

Metal oxide nanohybrids with uniform dimensions and controlled architectures possess unique compositional and structural superiorities, and thus harbor promising potential for a series of applications in energy, catalysis, and sensing systems. Herein, we propose a facile, general, and scalable cyano-bridged coordination polymer hydrogel-derived thermal-oxidation route for the construction of main-group metal and transition-metal heterometallic oxide nanohybrids with controlled constituents and architectures. The formation of Sn-Fe binary oxide nanohybrids has been demonstrated as an example by using cyano-bridged Sn(iv)-Fe(ii) bimetallic coordination polymer hydrogels (i.e., SnCl4-K4Fe(CN)6 cyanogels, Sn-Fe cyanogels) as precursors. The physicochemical properties of Sn-Fe cyanogels with different Sn/Fe ratios have been systematically examined, and it is found that perfect Sn-Fe cyanogels without unbridged Sn(iv) or Fe(ii) can be formed with Sn/Fe ratios from 2 : 1 to 1 : 2. More importantly, the simple adjustment of Sn/Fe ratios in the Sn-Fe cyanogel precursors can realize flexible dimensional control of the Sn-Fe binary oxide nanohybrids, and 2D/1D SnO2-Fe2O3 hierarchitectures, 2D SnO2-Fe2O3 nanosheets, and 3D SnO2-Fe2O3 networks have been synthesized using the Sn-Fe 1 : 2, Sn-Fe 1 : 1, and Sn-Fe 2 : 1 cyanogels as precursors, respectively. To demonstrate their compositional/structural superiorities and potential applications, the lithium-storage utilization of the Sn-Fe binary oxide nanohybrids has been selected as an objective application, and the nanohybrids exhibit Sn/Fe ratio-dependent lithium-storage performance. As a representative example, the 2D/1D SnO2-Fe2O3 hierarchitectures manifest markedly enhanced Li-storage performance in terms of reversible capacities and cycling stability in comparison with their constituent units, i.e., bare SnO2 nanosheets and Fe2O3 nanorods. The proposed cyanogel-derived thermal-oxidation strategy could

Two novel cyano-bridged heteropolynuclear complexes, [Co(3-aminopyridine)2Ni(μ-CN)2(CN)2]n and [Cu(3-aminopyridine)2Ni(μ-CN)2(CN)2]n have been synthesized and characterized by elemental, thermal, FT-IR and FT-Raman spectroscopies. The structures of complexes have been determined by X-ray powder diffraction. The FT-IR and FT-Raman spectra of complexes have been recorded in the region of 3500-400 cm-1 and 3500-100 cm-1, respectively. General information was acquired about structural properties of these complexes from FT-IR and FT-Raman spectra by considering changes at characteristic peaks of the cyano group and 3AP. The splitting of the ν(Ctbnd N) stretching bands in the FT-IR spectra for complexes indicates the presence of terminal and bridging cyanides. The thermal behaviors of these complexes have been also investigated in the range of 25-950 °C using TG and DTG methods. Magnetic susceptibility measurements were made at room temperature using Gouy-balance.

Metal oxide nanohybrids with uniform dimensions and controlled architectures possess unique compositional and structural superiorities, and thus harbor promising potential for a series of applications in energy, catalysis, and sensing systems. Herein, we propose a facile, general, and scalable cyano-bridged coordination polymer hydrogel-derived thermal-oxidation route for the construction of main-group metal and transition-metal heterometallic oxide nanohybrids with controlled constituents and architectures. The formation of Sn-Fe binary oxide nanohybrids has been demonstrated as an example by using cyano-bridged Sn(iv)-Fe(ii) bimetallic coordination polymer hydrogels (i.e., SnCl4-K4Fe(CN)6 cyanogels, Sn-Fe cyanogels) as precursors. The physicochemical properties of Sn-Fe cyanogels with different Sn/Fe ratios have been systematically examined, and it is found that perfect Sn-Fe cyanogels without unbridged Sn(iv) or Fe(ii) can be formed with Sn/Fe ratios from 2 : 1 to 1 : 2. More importantly, the simple adjustment of Sn/Fe ratios in the Sn-Fe cyanogel precursors can realize flexible dimensional control of the Sn-Fe binary oxide nanohybrids, and 2D/1D SnO2-Fe2O3 hierarchitectures, 2D SnO2-Fe2O3 nanosheets, and 3D SnO2-Fe2O3 networks have been synthesized using the Sn-Fe 1 : 2, Sn-Fe 1 : 1, and Sn-Fe 2 : 1 cyanogels as precursors, respectively. To demonstrate their compositional/structural superiorities and potential applications, the lithium-storage utilization of the Sn-Fe binary oxide nanohybrids has been selected as an objective application, and the nanohybrids exhibit Sn/Fe ratio-dependent lithium-storage performance. As a representative example, the 2D/1D SnO2-Fe2O3 hierarchitectures manifest markedly enhanced Li-storage performance in terms of reversible capacities and cycling stability in comparison with their constituent units, i.e., bare SnO2 nanosheets and Fe2O3 nanorods. The proposed cyanogel-derived thermal-oxidation strategy could open up new

Triazine compounds and cross-linked polymer compositions were made by heating aromatic nitriles to a temperature in the range of about 100 C to about 700 C, in the presence of a catalyst or mixture of catalysts. Aromatic nitrile-modified (terminated and/or appended) imide, benzimidazole, imidazopyrrolone, quinoxaline, and other condensation type prepolymers or their precopolymers were made which were trimerized with or without a filler by the aforementioned catalytic trimerization process.

Procedures for the purification and subsequent crystallization of the slightly soluble four-coordinate metallporphines, the simplest possible porphyrin derivatives, are described. Crystals of the porphine derivatives of cobalt(II), copper(II), platinum(II), and two polymorphs of zinc(II) were obtained. Analysis of the crystal and molecular structures shows that all except the platinum(II) derivative form an unusual trimeric species in the solid state. The isomorphous cobalt(II), copper(II), and one zinc(II) polymorph pack in the unit cell to form dimers as well as the trimers. Interplanar spacings between porphine rings are similar in both the dimers and trimers and range between 3.24 and 3.37 Å. Porphine rings are strongly overlapped with lateral shifts between ring centers in both the dimers and trimers with values between 1.52 and 1.70 Å or in Category S as originally defined by Scheidt and Lee. Periodic trends in the M-Np bond distances parallel those observed previously for tetraphenyl- and octaethylporphyrin derivatives. PMID:27276239

The kinetics of phenyl cyanate ester trimerization is studied in the bulk using differential scanning calorimetry. Dynamic experiments for different heating rates are analyzed for the activation energy using the model-free Kissinger-Akahira-Sunose(KAS) isoconversion method. The activation energy and other kinetic parameters are also obtained by fitting the dynamic data to a first order autocatalytic reaction model, which well describes the experimental data. The activation energy obtained from the KAS isoconversion method (70.1 kJ/mol) is in good agreement with that obtained from the kinetic model (73.2 kJ/mol) and is much lower than the more bulky cyanate esters studied in our laboratory, which have activation energies of approximately 95 kJ/mol. In addition, the rate constant for the phenyl cyanate ester is one to two orders higher than the bulkier cyanate esters in the temperature range of 200 to 300°C. Further elucidation of the dynamic experiments revealed a strong dependence of the reaction kinetics on the sample weight. Future work aims to understand this finding.

In recent years, structural studies have identified a number of bacterial, viral, and eukaryotic adhesive proteins that have a trimeric architecture. The prototype examples in bacteria are the Haemophilus influenzae Hia adhesin and the Yersinia enterocolitica YadA adhesin. Both Hia and YadA are members of the trimeric-autotransporter subfamily and are characterized by an internal passenger domain that harbors adhesive activity and a short C-terminal translocator domain that inserts into the outer membrane and facilitates delivery of the passenger domain to the bacterial surface. In this study, we examined the relationship between trimerization of the Hia and YadA passenger domains and the capacity for adhesive activity. We found that subunit-subunit interactions and stable trimerization are essential for native folding and stability and ultimately for full-level adhesive activity. These results raise the possibility that disruption of the trimeric architecture of trimeric autotransporters, and possibly other trimeric adhesins, may be an effective strategy to eliminate adhesive activity. PMID:16855229

The trimeric envelope spike of HIV-1 mediates virus entry into human cells. The exposed part of the trimer, gp140, consists of two noncovalently associated subunits, gp120 and gp41 ectodomain. A recombinant vaccine that mimics the native trimer might elicit entry-blocking antibodies and prevent virus infection. However, preparation of authentic HIV-1 trimers has been challenging. Recently, an affinity column containing the broadly neutralizing antibody 2G12 has been used to capture recombinant gp140 and prepare trimers from clade A BG505 that naturally produces stable trimers. However, this antibody-based approach may not be as effective for the diverse HIV-1 strains with different epitope signatures. Here, we report a new and simple approach to produce HIV-1 envelope trimers. The C terminus of gp140 was attached to Strep-tag II with a long linker separating the tag from the massive trimer base and glycan shield. This allowed capture of nearly homogeneous gp140 directly from the culture medium. Cleaved, uncleaved, and fully or partially glycosylated trimers from different clade viruses were produced. Extensive biochemical characterizations showed that cleavage of gp140 was not essential for trimerization, but it triggered a conformational change that channels trimers into correct glycosylation pathways, generating compact three-blade propeller-shaped trimers. Uncleaved trimers entered aberrant pathways, resulting in hyperglycosylation, nonspecific cross-linking, and conformational heterogeneity. Even the cleaved trimers showed microheterogeneity in gp41 glycosylation. These studies established a broadly applicable HIV-1 trimer production system as well as generating new insights into their assembly and maturation that collectively bear on the HIV-1 vaccine design. PMID:26088135

Many therapeutic proteins and protein subunit vaccines contain heterologous trimerization domains, such as the widely used GCN4-based isoleucine zipper (IZ) and the T4 bacteriophage fibritin foldon (Fd) trimerization domains. We found that these domains induced potent anti-IZ or anti-Fd antibody responses in animals when fused to an HIV-1 envelope glycoprotein (Env) immunogen. To dampen IZ-induced responses, we constructed an IZ domain containing four N-linked glycans (IZN4) to shield the underlying protein surface. When fused to two different vaccine antigens, HIV-1 Env and influenza hemagglutinin (HA), IZN4 strongly reduced the antibody responses against the IZ, but did not affect the antibody titers against Env or HA. Silencing of immunogenic multimerization domains with glycans might be relevant for therapeutic proteins and protein vaccines. PMID:25635058

Stable, artificial fibrous proteins that can be functionalized open new avenues in fields such as bionanomaterials design and fiber engineering. An important source of inspiration for the creation of such proteins are natural fibrous proteins such as collagen, elastin, insect silks, and fibers from phages and viruses. The fibrous parts of this last class of proteins usually adopt trimeric, β-stranded structural folds and are appended to globular, receptor-binding domains. It has been recently shown that the globular domains are essential for correct folding and trimerization and can be successfully substituted by a very small (27-amino acid) trimerization motif from phage T4 fibritin. The hybrid proteins are correctly folded nanorods that can withstand extreme conditions. When the fibrous part derives from the adenovirus fiber shaft, different tissue-targeting specificities can be engineered into the hybrid proteins, which therefore can be used as gene therapy vectors. The integration of such stable nanorods in devices is also a big challenge in the field of biomechanical design. The fibritin foldon domain is a versatile trimerization motif and can be combined with a variety of fibrous motifs, such as coiled-coil, collagenous, and triple β-stranded motifs, provided the appropriate linkers are used. The combination of different motifs within the same fibrous molecule to create stable rods with multiple functions can even be envisioned. We provide a comprehensive overview of the experimental procedures used for designing, creating, and characterizing hybrid fibrous nanorods using the fibritin trimerization motif.

We study low-temperature properties of atomic gases in trimerized optical kagome lattices. The laser arrangements that can be used to create these lattices are briefly described. We also present explicit results for the coupling constants of the generalized Hubbard models that can be realized in such lattices. In the case of a single-component Bose gas the existence of a Mott insulator phase with fractional numbers of particles per trimer is verified in a mean-field approach. The main emphasis of the paper is on an atomic spinless interacting Fermi gas in the trimerized kagome lattice with two fermions per site. This system is shown to be described by a quantum spin-1/2 model on the triangular lattice with couplings that depend on the bond directions. We investigate this model by means of exact diagonalization. Our key finding is that the system exhibits nonstandard properties of a quantum spin-liquid crystal: it combines planar antiferromagnetic order in the ground state with an exceptionally large number of low-energy excitations. The possibilities of experimental verification of our theoretical results are critically discussed.

HIV-1 entry into CD4(+) target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 angstroms of a soluble, cleaved Env trimer that is stabilized and antigenically near-native (termed the BG505 SOSIP.664 gp140 trimer) in complex with a potent broadly neutralizing antibody, PGT122. The structure shows a prefusion state of gp41, the interaction between the component gp120 and gp41 subunits, and how a close association between the gp120 V1/V2/V3 loops stabilizes the trimer apex around the threefold axis. The complete epitope of PGT122 on the trimer involves gp120 V1, V3, and several surrounding glycans. This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design. PMID:24179159

Burkholderia pseudomallei is a tier 1 select agent and the causative agent of melioidosis, a severe and often fatal disease with symptoms ranging from acute pneumonia and septic shock to a chronic infection characterized by abscess formation in the lungs, liver, and spleen. Autotransporters (ATs) are exoproteins belonging to the type V secretion system family, with many playing roles in pathogenesis. The genome of B. pseudomallei strain 1026b encodes nine putative trimeric AT proteins, of which only four have been described. Using a bioinformatic approach, we annotated putative domains within each trimeric AT protein, excluding the well-studied BimA protein, and found short repeated sequences unique to Burkholderia species, as well as an unexpectedly large proportion of ATs with extended signal peptide regions (ESPRs). To characterize the role of trimeric ATs in pathogenesis, we constructed disruption or deletion mutations in each of eight AT-encoding genes and evaluated the resulting strains for adherence to, invasion of, and plaque formation in A549 cells. The majority of the ATs (and/or the proteins encoded downstream) contributed to adherence to and efficient invasion of A549 cells. Using a BALB/c mouse model of infection, we determined the contributions of each AT to bacterial burdens in the lungs, liver, and spleen. At 48 h postinoculation, only one strain, Bp340::pDbpaC, demonstrated a defect in dissemination and/or survival in the liver, indicating that BpaC is required for wild-type virulence in this model. PMID:23716608

Despite its apparent simplicity and extensive theoretical investigations, the issue of what is the shape of the helium trimer is still debated in the literature. After reviewing previous conflicting interpretations of computational studies, we introduce the angle-angle distribution function as a tool to discuss in a simple way the shape of any trimer. We compute this function along with many different geometrical distributions using variational and diffusion Monte Carlo methods. We compare them with the corresponding ones for the neon and argon trimers. Our analysis shows that while Ne(3) and Ar(3) fluctuate around an equilibrium structure that is an equilateral triangle, (4)He(3) shows an extremely broad angle-angle distribution function, and all kinds of three-atom configurations must be taken into account in its description. Classifying (4)He(3) as either equilateral or linear or any other particular shape, as was done in the past, is not sensible, because in this case the intuitive notion of equilibrium structure is ill defined. Our results could help the interpretation of future experiments aimed at measuring the geometrical properties of the helium trimer. PMID:21894924

Adsorption of trimers and hexamers built of identical spheres was studied numerically using the random sequential adsorption (RSA) algorithm. Particles were adsorbed on a two-dimensional, flat and homogeneous surface. Numerical simulations allowed us to determine the maximal random coverage ratio, RSA kinetics as well as the available surface function (ASF), which is crucial for determining the kinetics of the adsorption process obtained experimentally. Additionally, the density autocorrelation function was measured. All the results were compared with previous results obtained for spheres, dimers and tetramers. PMID:24193213

We have investigated the energy dependence for the vibrational predissociation of ammonia trimer, (NH_3)_3 → (NH_3)_2 + NH_3, using infrared-action spectroscopy. The action spectra come from detecting specific rovibrational states of the monomer fragment via (2+1) resonance enhanced multiphoton excitation (REMPI) while scanning the IR excitation laser over the NH stretch transitions of the trimer as well as the dimer. The relative intensities of the dimer and trimer features in the action spectra depend on the amount of energy available for breaking the hydrogen bonds in the clusters. For example, the action spectra of ammonia fragments with large amounts of internal energy (v_2=3) show almost no trimer contribution since there is not enough energy available to break two bonds in the cyclic trimer. The action spectra for fragments with low internal energies (v_2=1), on the other hand, exhibit a substantial trimer component as more energy remains available to dissociate the cluster. Using the threshold at which the trimer feature becomes apparent in our spectra as an upper limit (Edissmax = hνvib-Eint(NH_3)), we determine the dissociation energy of ammonia trimer to be in the range between 1700-1800 cm-1. This range agrees well with theoretical predictions.

The effects of nanoconfinement on the reaction kinetics and properties of a monocyanate ester and the resulting cyanurate trimer are studied using differential scanning calorimetry (DSC). On the basis of both dynamic heating scans and isothermal reaction studies, the reaction rate is found to increase with decreasing nanopore size without a change in reaction mechanism. Both the monocyanate ester reactant and cyanurate product show reduced glass transition temperatures (T(g)s) as compared to the bulk; the T(g) depression increases with conversion and is more pronounced for the fully reacted product, suggesting that molecular stiffness influences the magnitude of nanoconfinement effects. Our results are consistent with the accelerated reaction and the T(g) depression found previously for the nanoconfined difunctional cyanate ester, supporting the supposition that intracyclization is not the origin of these effects. PMID:20496921

Broadly neutralizing antibodies (bnAbs) targeting the trimer apex of HIV envelope are favored candidates for vaccine design and immunotherapy because of their great neutralization breadth and potency. However, methods of isolating bnAbs against this site have been limited by the quaternary nature of the epitope region. Here we report the use of a recombinant HIV envelope trimer, BG505 SOSIP.664 gp140, as an affinity reagent to isolate quaternary-dependent bnAbs from the peripheral blood mononuclear cells of a chronically infected donor. The newly isolated bnAbs, named “PGDM1400–1412,” show a wide range of neutralization breadth and potency. One of these variants, PGDM1400, is exceptionally broad and potent with cross-clade neutralization coverage of 83% at a median IC50 of 0.003 µg/mL. Overall, our results highlight the utility of BG505 SOSIP.664 gp140 as a tool for the isolation of quaternary-dependent antibodies and reveal a mosaic of antibody responses against the trimer apex within a clonal family. PMID:25422458

Exact solutions for the low-temperature helium dimer and trimer, {sup 4}He{sub 2} and {sup 4}He{sub 3}, are derived, based on our {delta} function model for the interatomic potential. For the trimer, the Faddeev equations are shown to be separable in hyperspherical coordinates, with the S-wave alone giving an exact solution. The parameters {lambda}{sub 0} and r{sub 0} are fitted to accurate computations on the dimer and trimer. Excited states of the trimer are shown to exhibit the Efimov effect, whereby artificially reducing the strength of the two-body potential causes an infinite number of weakly-bound levels to condense out of the continuum. All the features anticipated by Efimov are quantitatively reproduced within our model. Since short-range details of the intermolecular forces are not relevant, our results can be considered to be universally applicable.

Assuring the microbiological safety of biological therapeutics remains an important concern. Our group has recently reported small trimeric peptides that have the ability to bind and remove a model non-enveloped virus, porcine parvovirus (PPV), from complex solutions containing human blood plasma. In an effort to improve the removal efficiency of these small peptides, we created a biased library of hexamer peptides that contain two previously reported trimeric peptides designated WRW and KYY. This library was screened and several hexamer peptides were discovered that also removed PPV from solution, but there was no marked improvement in removal efficiency when compared to the trimeric peptides. Based on simulated docking experiments, it appeared that hexamer peptide binding is dictated more by secondary structure, whereas the binding of trimeric peptides is dominated by charge and hydrophobicity. This study demonstrates that trimeric and hexameric peptides may have different, matrix-specific roles to play in virus removal applications. In general, the hexamer ligand may perform better for binding of specific viruses, whereas the trimer ligand may have more broadly reactive virus-binding properties. PMID:21751387

Allophycocyanin (APC), a cyanobacterial photosynthetic phycobiliprotein, functions in energy transfer as a light-harvesting protein. One of the prominent spectroscopic characteristics of APC is a strong red-shift in the absorption and emission maxima when monomers are assembled into a trimer. Previously, holo-APC alpha and beta subunits (holo-ApcA and ApcB) were successfully synthesized in Escherichia coli. In this study, both holo-subunits from Synechocystis sp. PCC 6803 were co-expressed in E. coli, and found to self-assemble into trimers. The recombinant APC trimer was purified by metal affinity and size-exclusion chromatography, and had a native structure identical to native APC, as determined by characteristic spectroscopic measurements, fluorescence quantum yield, tryptic digestion analysis, and molecular weight measurements. Combined with results from a study in which only the monomer was formed, our results indicate that bilin synthesis and the subsequent attachment to apo-subunits are important for the successful assembly of APC trimers. This is the first study to report on the assembly of recombinant ApcA and ApcB into a trimer with native structure. Our study provides a promising method for producing better fluorescent tags, as well as a method to facilitate the genetic analysis of APC trimer assembly and biological function. PMID:20607408

Bacteriorhodopsin (bR) trimers form a two-dimensional hexagonal lattice in the purple membrane of Halobacterium salinarum. However, the physiological significance of forming the lattice has long been elusive. Here, we study this issue by comparing properties of assembled and non-assembled bR trimers using directed mutagenesis, high-speed atomic force microscopy (HS-AFM), optical spectroscopy, and a proton pumping assay. First, we show that the bonds formed between W12 and F135 amino acid residues are responsible for trimer-trimer association that leads to lattice assembly; the lattice is completely disrupted in both W12I and F135I mutants. HS-AFM imaging reveals that both crystallized D96N and non-crystallized D96N/W12I mutants undergo a large conformational change (i.e., outward E-F loop displacement) upon light-activation. However, lattice disruption significantly reduces the rate of conformational change under continuous light illumination. Nevertheless, the quantum yield of M-state formation, measured by low-temperature UV-visible spectroscopy, and proton pumping efficiency are unaffected by lattice disruption. From these results, we conclude that trimer-trimer association plays essential roles in providing bound retinal with an appropriate environment to maintain its full photo-reactivity and in maintaining the natural photo-reaction pathway. PMID:23462099

The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained. PMID:27294109

The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained. PMID:27294109

Chiral conglomerates of domains with opposite handedness have attracted much attention from researchers. We prepared a homologous series of achiral liquid crystal trimers in which two phenylpyrimidine units and one biphenyl unit were connected via flexible methylene spacers. We investigated their phase transition behaviour. Some trimers possessing odd-numbered spacers were found to exhibit a nematic phase and a dark chiral conglomerate phase possessing a layered structure. The chiral characteristics were confirmed by uncrossing the polarizers in opposite directions. The layer spacing detected using X-ray diffraction was about 80% of the molecular length. The structure-property relations indicate that intermolecular interactions cause a conformational change in the trimers possessing flexible odd-numbered methylene spacers to form helical conformers with axial chirality, which might induce chiral segregation and layer deformation to drive the chiral conglomerates. PMID:26947890

Infrared spectra of N_{2}O trimers are studied using a tunable diode laser to probe a pulsed supersonic slit-jet expansion. A previous observation by R.E. Miller and L. Pedersen [J. Chem. Phys. 108, 436 (1998)] in the N_{2}O νb{1}+νb{3} combination band region ( 3480 cm^{-1}) showed the trimer structure to be noncyclic, with three inequivalent N_{2}O monomer units which could be thought of as an N_{2}O dimer (slipped antiparallel configuration) plus a third monomer unit lying above the dimer plane. The present observations cover the N_{2}O fundamental band regions νb{3} ( 1280 cm^{-1}) and νb{1} ( 2230 cm^{-1}). In the νb{3} region, two trimer bands are assigned with vibrational shifts and other characteristics similar to those in the νb{1}+νb{3} region, but in the νb{1} region all three possible trimer bands are observed. Relationships among the various bands such as rotational intensity patterns, vibrational shifts, and the properties of the related N_{2}O dimer, generally support the conclusions of Miller and Pedersen. Three trimer bands are also observed for the fully ^{15}N-substituted species in the νb{1} region, and these results should aid in detection of the as-yet-unobserved pure rotational microwave spectrum of the trimer. Finally, three combination bands involving the intermolecular van der Waals modes at 2253.7, 2255.5, and 2269.4 cm^{-1} have been measured. The analyses of these bands and the identification of the nature of the intermolecular modes involved are currently underway.

Ab initio and density functional theory calculations with aug-cc-pVDZ and aug-cc-pVTZ basis sets have been performed on the HCl -CH3SH dimer and HCl -(CH3SH)2 and (HCl)2-CH3SH trimers. Structures, energetics, and infrared frequencies are calculated. The results are discussed in terms of the cooperativity effect which is a characteristic of H-bonded systems and compared to oxygen-containing analogs of the same trimers, HCl -(CH3OH)2 and (HCl)2-CH3OH, which have been published recently.

By the oxidation of the hexafluoropropylene trimers with an aqueous solution of sodium hypochlorite in the presence of acetonitrile the following ..cap alpha..-oxides were obtained: 2,3-Epoxyperfluoro-3-isopropyl-4-methylpentane and 2,3-epoxyperfluoro-3-ethyl-2,4-dimethylpentane. According to the /sup 19/F NMR data, the epoxidation takes place stereoselectively with the formation of only one conformer of the ..cap alpha..-oxide in each case. The determining effect of the steric factors on the reactivity of the oxides of hexafluoropropylene trimers in reaction with nucleophiles was demonstrated.

Background The recent swine-origin H1N1 pandemic illustrates the need to develop improved procedures for rapid production of influenza vaccines. One alternative to the current egg-based manufacture of influenza vaccine is to produce a hemagglutinin (HA) subunit vaccine using a recombinant expression system with the potential for high protein yields, ease of cloning new antigenic variants, and an established safety record in humans. Methodology/Principal Findings We generated a soluble HA (sHA), derived from the H3N2 virus A/Aichi/2/68, modified at the C-terminus with a GCN4pII trimerization repeat to stabilize the native trimeric structure of HA. When expressed in the baculovirus system, the modified sHA formed native trimers. In contrast, the unmodified sHA was found to present epitopes recognized by a low-pH conformation specific monoclonal antibody. We found that mice primed and boosted with 3 µg of trimeric sHA in the absence of adjuvants had significantly higher IgG and HAI titers than mice that received the unmodified sHA. This correlated with an increased survival and reduced body weight loss following lethal challenge with mouse-adapted A/Aichi/2/68 virus. In addition, mice receiving a single vaccination of the trimeric sHA in the absence of adjuvants had improved survival and body weight loss compared to mice vaccinated with the unmodified sHA. Conclusions/Significance Our data indicate that the recombinant trimeric sHA presents native trimeric epitopes while the unmodified sHA presents epitopes not exposed in the native HA molecule. The epitopes presented in the unmodified sHA constitute a “silent face” which may skew the antibody response to epitopes not accessible in live virus at neutral pH. The results demonstrate that the trimeric sHA is a more effective influenza vaccine candidate and emphasize the importance of structure-based antigen design in improving recombinant HA vaccines. PMID:20824188

The trimeric HIV-1 envelope glycoprotein (Env) is critical for host immune recognition and neutralization. Despite advances in trimer design, the roots of Env trimer metastability remain elusive. Here we investigate the contribution of two Env regions to metastability. First, we computationally redesign a largely disordered bend in heptad region 1 (HR1) of SOSIP trimers that connects the long, central HR1 helix to the fusion peptide, substantially improving the yield of soluble, well-folded trimers. Structural and antigenic analyses of two distinct HR1 redesigns confirm that redesigned Env closely mimics the native, prefusion trimer with a more stable gp41. Next, we replace the cleavage site between gp120 and gp41 with various linkers in the context of an HR1 redesign. Electron microscopy reveals a potential fusion intermediate state for uncleaved trimers containing short but not long linkers. Together, these results outline a general approach for stabilization of Env trimers from diverse HIV-1 strains. PMID:27349805

The trimeric HIV-1 envelope glycoprotein (Env) is critical for host immune recognition and neutralization. Despite advances in trimer design, the roots of Env trimer metastability remain elusive. Here we investigate the contribution of two Env regions to metastability. First, we computationally redesign a largely disordered bend in heptad region 1 (HR1) of SOSIP trimers that connects the long, central HR1 helix to the fusion peptide, substantially improving the yield of soluble, well-folded trimers. Structural and antigenic analyses of two distinct HR1 redesigns confirm that redesigned Env closely mimics the native, prefusion trimer with a more stable gp41. Next, we replace the cleavage site between gp120 and gp41 with various linkers in the context of an HR1 redesign. Electron microscopy reveals a potential fusion intermediate state for uncleaved trimers containing short but not long linkers. Together, these results outline a general approach for stabilization of Env trimers from diverse HIV-1 strains.

The trimeric HIV-1 envelope glycoprotein (Env) is critical for host immune recognition and neutralization. Despite advances in trimer design, the roots of Env trimer metastability remain elusive. Here we investigate the contribution of two Env regions to metastability. First, we computationally redesign a largely disordered bend in heptad region 1 (HR1) of SOSIP trimers that connects the long, central HR1 helix to the fusion peptide, substantially improving the yield of soluble, well-folded trimers. Structural and antigenic analyses of two distinct HR1 redesigns confirm that redesigned Env closely mimics the native, prefusion trimer with a more stable gp41. Next, we replace the cleavage site between gp120 and gp41 with various linkers in the context of an HR1 redesign. Electron microscopy reveals a potential fusion intermediate state for uncleaved trimers containing short but not long linkers. Together, these results outline a general approach for stabilization of Env trimers from diverse HIV-1 strains. PMID:27349805

Aromatic nitriles may be trimerized at moderate temperature and pressure with p-toluenesulfonic acid as catalyst. Studies were conducted to establish the effect of the reaction temperature, pressure, time, and catalyst concentration on yield of the trimerized product. Trimerization studies were also conducted to establish the effect of substituting electron donating or withdrawing groups on benzonitrile. Preliminary results of using the catalytic trimerization approach to prepare s-triazine cross-linked polyimide/graphite fiber composites are presented.

Diffusion barriers for a cluster of three water molecules on Pd{111} have been estimated from ab-initio Density Functional Theory. A model for the diffusion of a cluster of three water molecules (trimer) based in rotations yields a simple explanation of why the cluster can diffuse faster than a single water molecule by a factor ≈ 102 [1]. This model is based on the differences between the adsorption geometry for the three molecules forming the trimer. One member interacts strongly with the surface and sits closer to the surface (d) while the other two interact weakly and stay at a larger separation from the surface (u). The trimer rotates nearly freely around the axis determined by the d-like monomer. Translations of the whole trimer imply breaking the strong interaction of the d-like molecule with the surface with a high energy cost. Alternatively, thermal fluctuations can exchange the position of the molecule sitting closer to the surface with a lower energetic cost. Rotations around different axis yield a diffusion mechanism where the strong interaction is maintained along the diffusion path, therefore lowering the effective activation barrier.

The human immunodeficiency virus type 1 (HIV-1) exterior envelope glycoprotein, gp120, mediates binding to the viral receptors and, along with the transmembrane glycoprotein gp41, is a major target for neutralizing antibodies. We asked whether replacing the gp41 fusion/trimerization domain with a stable trimerization motif might lead to a more stable gp120 trimer that would be amenable to structural and immunologic analysis. To obtain stable gp120 trimers, a heterologous trimerization motif, GCN4, was appended to the C terminus of YU2gp120. Biochemical analysis indicated that the gp120-GCN4 trimers were superior to gp140 molecules in their initial homogeneity, and trilobed structures were observable by electron microscopy. Biophysical analysis of gp120-GCN4 trimers by isothermal titration calorimetry (ITC) and ultracentrifugation analyses indicated that most likely two molecules of soluble CD4 could bind to one gp120-GCN4 trimer. To further examine restricted CD4 stoichiometric binding to the gp120-GCN4 trimers, we generated a low-affinity CD4 binding trimer by introducing a D457V change in the CD4 binding site of each gp120 monomeric subunit. The mutant trimers could definitively bind only one soluble CD4 molecule, as determined by ITC and sedimentation equilibrium centrifugation. These data indicate that there are weak interactions between the gp120 monomeric subunits of the GCN4-stabilized trimers that can be detected by low-affinity ligand sensing. By similar analysis, we also determined that removal of the variable loops V1, V2, and V3 in the context of the gp120-GCN4 proteins allowed the binding of three CD4 molecules per trimer. Interestingly, both the gp120-GCN4 variants displayed a restricted stoichiometry for the CD4-induced antibody 17b of one antibody molecule binding per trimer. This restriction was not evident upon removal of the variable loops V1 and V2 loops, consistent with conformational constraints in the wild-type gp120 trimers and similar to

Summary The envelope glycoprotein trimer mediates HIV-1 entry into cells. The trimer is flexible, fluctuating between closed and more open conformations and sometimes sampling the fully open, CD4-bound form. We hypothesized that conformational flexibility could hinder the induction of broadly neutralizing antibodies (bNAbs). We therefore modified soluble Env trimers to stabilize their closed, ground states. The trimer variants were indeed stabilized in the closed conformation, with a reduced ability to undergo receptor-induced conformational changes and a decreased exposure of non-neutralizing V3-directed antibody epitopes. In rabbits, the stabilized trimers induced similar autologous Tier-1B or Tier-2 NAb titers to those elicited by the corresponding wild-type trimers, but lower levels of V3-directed Tier-1A NAbs. Stabilized, closed trimers might therefore be useful components of vaccines aimed at inducing bNAbs. PMID:26687358

The envelope glycoprotein trimer mediates HIV-1 entry into cells. The trimer is flexible, fluctuating between closed and more open conformations and sometimes sampling the fully open, CD4-bound form. We hypothesized that conformational flexibility and transient exposure of non-neutralizing, immunodominant epitopes could hinder the induction of broadly neutralizing antibodies (bNAbs). We therefore modified soluble Env trimers to stabilize their closed, ground states. The trimer variants were indeed stabilized in the closed conformation, with a reduced ability to undergo receptor-induced conformational changes and a decreased exposure of non-neutralizing V3-directed antibody epitopes. In rabbits, the stabilized trimers induced similar autologous Tier-1B or Tier-2 NAb titers to those elicited by the corresponding wild-type trimers but lower levels of V3-directed Tier-1A NAbs. Stabilized, closed trimers might therefore be useful components of vaccines aimed at inducing bNAbs. PMID:26687358

The inelastic response of a bosonic trimer is explored in the confines of the Borromean region. To this end we model the interaction between the external field and the bosonic system as a photoabsorptionlike process and study the response of the trimer in the quadrupole approximation. We utilize the hyperspherical-harmonics expansion to solve the Schrödinger equation and the Lorentz integral transform method to calculate the reaction. It is found that the magnitude of the response function and corresponding sum rules increase exponentially when approaching the 3-body threshold. It is also found that this increase is governed by unnatural exponents. The connection between our results and radio-frequency experiments in ultracold atom systems is made. PMID:22540468

Two new cerebrosides, ferocerebrosides A (1) [(2S,3R,4E,8E,2'R)-1-O-(beta-glucopyranosyl)-N-(2'-hydroxydocosanoyl)-4,8-sphingadienine] and B (2) [(2S,3R,4E,8E,2'R)-1-O-(beta-glucopyranosyl)-N-(2'-hydroxytetracosanoyl)-4,8-sphingadienine], two new tocopherol trimers, ferotocotrimers C (5) and D (6), and two known tocopherol trimers, IVb (3) and IVa (4), were isolated from the seeds of Euryale ferox. Their structures were determined on the basis of spectroscopic data, especially 1D and 2D NMR experiments. Compounds 1 and 2 showed cytotoxicity in the brine shrimp lethality bioassay, with LC50 values of 0.17 and 0.20 mM, respectively. PMID:17567070

We report that NO molecules unexpectedly prefer a trimeric configuration on Cu(111). We used scanning tunneling microscopy (STM) at 6 K, and confirmed that the NO molecule is bonded to the face-centered-cubic hollow site in an upright configuration. The individual NO molecule is imaged as a ring protrusion, which is characteristic of the doubly degenerate 2π{sup *} orbital. A triangular trimer is thermodynamically more favorable than the monomer and dimer, and its bonding structure was characterized by STM manipulation. This unique behavior of NO on Cu(111) is ascribed to the threefold symmetry of the surface, facilitating effective mixing of the 2π{sup *} orbitals in a triangular configuration.

Treatment of periodontal disease is a complex and multidisciplinary procedure, requiring periodontal, surgical, restorative, and orthodontic treatment modalities. Several authors attempted to formulate models for periodontal treatment that orders the treatment steps in a logical and easy to remember manner. In this article, we discuss two models of periodontal treatment planning from two of the most well-known textbook in the specialty of periodontics internationally. Then modify them to arrive at a new model of periodontal treatment planning, The Trimeric Model. Adding restorative and orthodontic interrelationships with periodontal treatment allows us to expand this model into the Extended Trimeric Model of periodontal treatment planning. These models will provide a logical framework and a clear order of the treatment of periodontal disease for general practitioners and periodontists alike. PMID:25177662

We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.

We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green's function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states. PMID:26671378

The authors report a study of the allophycocyanin trimer (APC), a light-harvesting protein complex from cyanobacteria, by room-temperature single-molecule measurements of fluorescence spectra, lifetimes, intensity trajectories, and polarization modulation. Emission spectra of individual APC trimers are found to be homogeneous on the time scale of seconds. In contrast, their emission lifetimes are found to be widely distributed because of generation of long-lived exciton traps during the course of measurements. The intensity trajectories and polarization modulation experiments indicate reversible exciton trap formation within the three quasi-independent pairs of strong interacting {alpha}84 and {beta}84 chromophores in APC, as well as photobleaching of individual chromophores. Comparison experiments under continuous-wave and pulsed excitation reveal a two-photon mechanism for generating exciton traps and/or photobleaching, which involves exciton-exciton annihilation. These single-molecule experiments provide new insights into the spectroscopy, exciton dynamics, and photochemistry of light-harvesting complexes.

With the help of the time-dependent local-density approximation (TDLDA) coupled non-adiabatically to molecular dynamics (MD), we studied both the static properties and irradiation dynamics of water trimer subject to the short and intense femtosecond laser field. It is shown that the optimized geometry and the optical absorption strength of the water trimer accord well with results in literature. Three typical possible irradiated scenarios of water trimer which are “normal oscillation”, “dissociation and formation” and “pure OH dissociation” are exhibited by investigating the ionization and the level depletion related to electrons as well as the OH bonds, proton-transfer, the intermolecular distance and the kinetic energy connected with ions. In three scenarios, the behaviors of water trimer can be attributed to the sequential combination of responses of the electrons emission, the proton-transfer, OH vibration and rotation, OH dissociation and hydroxyl formation, respectively. The relevant time scales of the first proton-transfer and OH dissociation are identified as 13 fs and 10-20 fs, respectively. The study of kinetic energies of ions show that the kinetic energies of the remaining ions are all below 4.5 eV and outgoing hydrogen ions carry a kinetic energy about 5-12 eV. Furthermore, it is found that in the tunneling ionization situations the depletion is fairly shared between the various levels except the most deep occupied electronic level while in the multiphotonic ionization case the electron loss comes from all single-electron levels and the HOMO level contributes the most.

We present exact models for an antiferromagnetic S=1 spin chain describing trimerization as well as for an antiferromagnetic S=3/2 spin chain describing tetramerization. These models can be seen as generalizations of the Majumdar-Ghosh model. For both models, we provide a local Hamiltonian and its exact threefold or fourfold degenerate ground state wave functions, respectively. We numerically confirm the validity of both models using exact diagonalization and discuss the low-lying excitations.

We study low-temperature properties of atomic gases in trimerized optical kagomé lattices. The laser arrangements that can be used to create these lattices are briefly described. We also present explicit results for the coupling constants of the generalized Hubbard models that can be realized in such lattices. In the case of a single-component Bose gas the existence of a Mott insulator phase with fractional numbers of particles per trimer is verified in a mean-field approach. The main emphasis of the paper is on an atomic spinless interacting Fermi gas in the trimerized kagomé lattice with two fermions per site. This system is shown to be described by a quantum spin- 1/2 model on the triangular lattice with couplings that depend on the bond directions. We investigate this model by means of exact diagonalization. Our key finding is that the system exhibits nonstandard properties of a quantum spin-liquid crystal: it combines planar antiferromagnetic order in the ground state with an exceptionally large number of low-energy excitations. The possibilities of experimental verification of our theoretical results are critically discussed.

The matrix (MA) domain of HIV Gag has important functions in directing the trafficking of Gag to sites of assembly and mediating the incorporation of the envelope glycoprotein (Env) into assembling particles. HIV-1 MA has been shown to form trimers in vitro; however, neither the presence nor the role of MA trimers has been documented in HIV-1 virions. We developed a cross-linking strategy to reveal MA trimers in virions of replication-competent HIV-1. By mutagenesis of trimer interface residues, we demonstrated a correlation between loss of MA trimerization and loss of Env incorporation. Additionally, we found that truncating the long cytoplasmic tail of Env restores incorporation of Env into MA trimer-defective particles, thus rescuing infectivity. We therefore propose a model whereby MA trimerization is required to form a lattice capable of accommodating the long cytoplasmic tail of HIV-1 Env; in the absence of MA trimerization, Env is sterically excluded from the assembling particle. These findings establish MA trimerization as an obligatory step in the assembly of infectious HIV-1 virions. As such, the MA trimer interface may represent a novel drug target for the development of antiretrovirals. PMID:26711999

We study the light scattering by plasmonic and dielectric symmetric trimers to investigate the existence of polarization-independent Fano resonances. Plasmonic hybridization theory is revealed to hide simple physics, and we instead provide a simplified model for hybridization to derive a plasmonic trimer's eigenmodes analytically. This approach is demonstrated to accurately recreate full wave simulations of plasmonic trimers and their Fano resonances. We are subsequently able to deduce the grounds for modal interference in plasmonic trimers and the related formation of Fano resonances. However, by generalizing our simplified hybridization approach, we are also able to investigate the eigenmodes of all-dielectric trimers. We show that bianisotropic coupling channels between high-index dielectric nanoparticles are able to increase the capacity for Fano resonances, even at normal incidence. We finally provide the first experimental measurements of sharp, polarization-independent Fano resonances from a symmetric all-dielectric trimer, with very good agreement with the predicted response from our simplified hybridization theory.

We Coulomb explode argon and neon dimers, trimers, and tetramers by multiple ionization in an ultrashort 800 nm laser pulse. By measuring all momentum vectors of the singly charged ions in coincidence, we determine the ground state nuclear wave function of the dimer, trimer, and tetramer. Furthermore we retrieve the bond angles of the trimer in position space by applying a classical numerical simulation. For the argon and neon trimer, we find a structure close to the equilateral triangle. The width of the distribution around the equilateral triangle is considerably wider for neon than for argon. PMID:21413773

There has been confusion about the subunit stoichiometry of the degenerin family of ion channels. Recently, a crystal structure of acid-sensing ion channel (ASIC) 1a revealed that it assembles as a trimer. Here, we used atomic force microscopy (AFM) to image unprocessed ASIC1a bound to mica. We detected a mixture of subunit monomers, dimers and trimers. In some cases, triple-subunit clusters were clearly visible, confirming the trimeric structure of the channel, and indicating that the trimer sometimes disaggregated after adhesion to the mica surface. This AFM-based technique will now enable us to determine the subunit arrangement within heteromeric ASICs.

Acinetobacter baumannii has recently emerged as a highly troublesome nosocomial pathogen, especially in patients in intensive care units and in those undergoing mechanical ventilation. We have identified a surface protein adhesin of A. baumannii, designated the Acinetobacter trimeric autotransporter (Ata), that contains all of the typical features of trimeric autotransporters (TA), including a long signal peptide followed by an N-terminal, surface-exposed passenger domain and a C-terminal domain encoding 4 β-strands. To demonstrate that Ata encoded a TA, we created a fusion protein in which we replaced the entire passenger domain of Ata with the epitope tag V5, which can be tracked with specific monoclonal antibodies, and demonstrated that the C-terminal 101 amino acids of Ata were capable of exporting the heterologous V5 tag to the surface of A. baumannii in a trimeric form. We found that Ata played a role in biofilm formation and bound to various extracellular matrix/basal membrane (ECM/BM) components, including collagen types I, III, IV, and V and laminin. Moreover, Ata mediated the adhesion of whole A. baumannii cells to immobilized collagen type IV and played a role in the survival of A. baumannii in a lethal model of systemic infection in immunocompetent mice. Taken together, these results reveal that Ata is a TA of A. baumannii involved in virulence, including biofilm formation, binding to ECM/BM proteins, mediating the adhesion of A. baumannii cells to collagen type IV, and contributing to the survival of A. baumannii in a mouse model of lethal infection. PMID:22609912

We investigate in vitro fibrillation kinetics of the hormone peptide glucagon at various concentrations using confocal microscopy and determine the glucagon fibril persistence length 60μm. At all concentrations we observe that periods of individual fibril growth are interrupted by periods of stasis. The growth probability is large at high and low concentrations and is reduced for intermediate glucagon concentrations. To explain this behavior we propose a simple model, where fibrils come in two forms, one built entirely from glucagon monomers and one entirely from glucagon trimers. The opposite building blocks act as fibril growth blockers, and this generic model reproduces experimental behavior well.

We present a combined experimental and theoretical study to investigate the spatial distribution of photoelectrons emitted from core-shell silver (Ag) nanoparticles. We use two-photon photoemission microscopy (2P-PEEM) to spatially resolve electron emission from a trimeric core-shell aggregate of triangular symmetry. Finite difference time domain (FDTD) simulations are performed to model the intensity distributions of the electromagnetic near-fields resulting from femtosecond (fs) laser excitation of localized surface plasmon oscillations in the triangular core-shell structure. We demonstrate that the predicted FDTD near-field intensity distribution reproduces the 2P-PEEM photoemission pattern.

ABSTRACT Recombinant trimeric mimics of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) spike should expose as many epitopes as possible for broadly neutralizing antibodies (bNAbs) but few, if any, for nonneutralizing antibodies (non-NAbs). Soluble, cleaved SOSIP.664 gp140 trimers based on the subtype A strain BG505 approach this ideal and are therefore plausible vaccine candidates. Here, we report on the production and in vitro properties of a new SOSIP.664 trimer derived from a subtype B env gene, B41, including how to make this protein in low-serum media without proteolytic damage (clipping) to the V3 region. We also show that nonclipped trimers can be purified successfully via a positive-selection affinity column using the bNAb PGT145, which recognizes a quaternary structure-dependent epitope at the trimer apex. Negative-stain electron microscopy imaging shows that the purified, nonclipped, native-like B41 SOSIP.664 trimers contain two subpopulations, which we propose represent an equilibrium between the fully closed and a more open conformation. The latter is different from the fully open, CD4 receptor-bound conformation and may represent an intermediate state of the trimer. This new subtype B trimer adds to the repertoire of native-like Env proteins that are suitable for immunogenicity and structural studies. IMPORTANCE The cleaved, trimeric envelope protein complex is the only neutralizing antibody target on the HIV-1 surface. Many vaccine strategies are based on inducing neutralizing antibodies. For HIV-1, one approach involves using recombinant, soluble protein mimics of the native trimer. At present, the only reliable way to make native-like, soluble trimers in practical amounts is via the introduction of specific sequence changes that confer stability on the cleaved form of Env. The resulting proteins are known as SOSIP.664 gp140 trimers, and the current paradigm is based on the BG505 subtype A env gene. Here, we describe the

Opalescence, sometimes observed in antibody solutions, is thought to be mediated by light scattering of soluble oligomers or insoluble particulates. However, mechanistic features, such as stoichiometry and self-association affinity of oligomeric species related to opalescence, are poorly understood. Here, opalescence behavior of a monoclonal antibody (mAb-1) solution was studied over a wide range of solution conditions including different protein concentrations, pH, and in the presence or absence of salt. Hydrodynamic and thermodynamic properties of mAb-1 solutions were studied by analytical ultracentrifugation and dynamic light scattering. Opalescence in mAb-1 solutions is pH and concentration dependent. The degree of opalescence correlates with reversible monomer-trimer equilibrium detected by analytical ultracentrifugation. Increased trimer formation corresponds to increased opalescence in mAb-1 solutions at higher pH and protein concentrations. Addition of NaCl shifts this equilibrium toward monomer and reduces solution opalescence. This study demonstrates that opalescence in mAb-1 solutions does not arise from the light scattering of monomer or random molecular self-associations but is strongly correlated with a specific self-association stoichiometry and affinity. Importantly, at pH 5.5 (far below isoelectric point of mAb-1), the solution is not opalescent and with nonideal behavior. This study also dissects several parameters to describe the hydrodynamic and thermodynamic nonideality. PMID:27373839

Background Pathogenic bacteria adhere to the host cell surface using a family of outer membrane proteins called Trimeric Autotransporter Adhesins (TAAs). Although TAAs are highly divergent in sequence and domain structure, they are all conceptually comprised of a C-terminal membrane anchoring domain and an N-terminal passenger domain. Passenger domains consist of a secretion sequence, a head region that facilitates binding to the host cell surface, and a stalk region. Methodology/Principal Findings Pathogenic species of Burkholderia contain an overabundance of TAAs, some of which have been shown to elicit an immune response in the host. To understand the structural basis for host cell adhesion, we solved a 1.35 Å resolution crystal structure of a BpaA TAA head domain from Burkholderia pseudomallei, the pathogen that causes melioidosis. The structure reveals a novel fold of an intricately intertwined trimer. The BpaA head is composed of structural elements that have been observed in other TAA head structures as well as several elements of previously unknown structure predicted from low sequence homology between TAAs. These elements are typically up to 40 amino acids long and are not domains, but rather modular structural elements that may be duplicated or omitted through evolution, creating molecular diversity among TAAs. Conclusions/Significance The modular nature of BpaA, as demonstrated by its head domain crystal structure, and of TAAs in general provides insights into evolution of pathogen-host adhesion and may provide an avenue for diagnostics. PMID:20862217

We propose and numerically verify a scheme for compact optical modulation which can enable complex directional switching of signals in integrated micro-optical circuits within hundreds of femtoseconds. The scheme is based on a trimer comprised of two identical silica whispering gallery mode (WGM) microresonators spaced by a central non-linear WGM resonator. The non-linear resonator is in the form of a silica cylinder with a thin coating of an ultrafast Kerr nonlinear material (a J-aggregate of cyanine dye). Using a two-dimensional finite-difference time-domain method and realistic material and structural parameters, we investigated the near-field coupling from a waveguide to the trimer and the subsequent switching process. In our scheme the sandwiched central control resonator has a resonant frequency that is mismatched to that of the input and output resonators. Therefore the optical energy is coupled from the waveguide into only the primary resonator in linear operation. However, for control light intensities of more than approximately 10(-2) W/microm the effective index and hence eigenfrequency of the central resonator can be shifted to match that of its neighbors and hence the optical energy can be redirected. PMID:20052247

This work presents a comprehensive quantum dynamics calculation of the bound rovibrational eigenstates of argon trimer (Ar{sub 3}), using the ScalIT suite of parallel codes. The Ar{sub 3} rovibrational energy levels are computed to a very high level of accuracy (10{sup −3} cm{sup −1} or better), and up to the highest rotational and vibrational excitations for which bound states exist. For many of these rovibrational states, wavefunctions are also computed. Rare gas clusters such as Ar{sub 3} are interesting because the interatomic interactions manifest through long-range van der Waals forces, rather than through covalent chemical bonding. As a consequence, they exhibit strong Coriolis coupling between the rotational and vibrational degrees of freedom, as well as highly delocalized states, all of which renders accurate quantum dynamical calculation difficult. Moreover, with its (comparatively) deep potential well and heavy masses, Ar{sub 3} is an especially challenging rare gas trimer case. There are a great many rovibrational eigenstates to compute, and a very high density of states. Consequently, very few previous rovibrational state calculations for Ar{sub 3} may be found in the current literature—and only for the lowest-lying rotational excitations.

This work presents a comprehensive quantum dynamics calculation of the bound rovibrational eigenstates of argon trimer (Ar3), using the ScalIT suite of parallel codes. The Ar3 rovibrational energy levels are computed to a very high level of accuracy (10(-3) cm(-1) or better), and up to the highest rotational and vibrational excitations for which bound states exist. For many of these rovibrational states, wavefunctions are also computed. Rare gas clusters such as Ar3 are interesting because the interatomic interactions manifest through long-range van der Waals forces, rather than through covalent chemical bonding. As a consequence, they exhibit strong Coriolis coupling between the rotational and vibrational degrees of freedom, as well as highly delocalized states, all of which renders accurate quantum dynamical calculation difficult. Moreover, with its (comparatively) deep potential well and heavy masses, Ar3 is an especially challenging rare gas trimer case. There are a great many rovibrational eigenstates to compute, and a very high density of states. Consequently, very few previous rovibrational state calculations for Ar3 may be found in the current literature-and only for the lowest-lying rotational excitations. PMID:25053315

We study theoretically a triangular cluster of three magnetic impurities, hybridizing locally with conduction electrons of a metallic host. Such a cluster is the simplest to exhibit frustration, an important generic feature of many complex molecular systems in which different interactions compete. Here, low-energy doublet states of the trimer are favored by effective exchange interactions produced by strong electronic repulsion in localized impurity orbitals. Parity symmetry protects a level crossing of such states on tuning microscopic parameters, while an avoided crossing arises in the general distorted case. Upon coupling to a metallic host, the behavior is shown to be immensely rich because collective quantum many-body effects now also compete. In particular, impurity degrees of freedom are totally screened at low temperatures in a Kondo-screened Fermi liquid phase, while degenerate ground states persist in a local moment phase. Local frustration drives the quantum phase transition between the two, which may be first order or of Kosterlitz-Thouless type, depending on symmetries. Unusual mechanisms for local moment formation and Kondo screening are found due to the orbital structure of the impurity trimer. Our results are of relevance for triple quantum dot devices. The problem is studied by a combination of analytical arguments and the numerical renormalization group. PMID:23527540

The major light-harvesting complex (LHCII) of photosystem II, the most abundant chlorophyll-containing complex in higher plants, is organized in trimers. In this paper we show that the trimerization of LHCII occurs spontaneously and is dependent on the presence of lipids. LHCII monomers were reconstituted from the purified apoprotein (LHCP), overexpressed in Escherichia coli, and pigments, purified from chloroplast membranes. These synthetic LHCII monomers trimerize in vitro in the presence of a lipid fraction isolated from pea thylakoids. The reconstituted LHCII trimers are very similar to native LHCII trimers in that they are stable in the presence of mild detergents and can be isolated by partially denaturing gel electrophoresis or by centrifugation in sucrose density gradients. Moreover, both native and reconstituted LHCII trimers exhibit signals in circular dichroism in the visible range that are not seen in native or reconstituted LHCII monomers, indicating that trimer formation either establishes additional pigment-pigment interactions or alters pre-existing interactions. Reconstituted LHCII trimers readily form two-dimensional crystals that appear to be identical to crystals of the native complex. Images PMID:8062818

We investigate the magnetic interactions within a graphene superlattice produced by three directly substituted transition-metal atoms (specifically chromium and manganese). Using a first principles approach, we calculate the electronic and magnetic properties for this system assuming an equilateral trimer configuration with varying atomic separations. Through an examination of the electronic band structure, density of states, and Millikan populations (magnetic moment) for each atom, we find that the presence of magnetic impurities establishes a distinct magnetic moment in the graphene lattice, where the interactions are dependent on the spatial and magnetic characteristic between the magnetic atoms and the carbon atoms, which leads to either ferromagnetic or antiferromagnetic behavior. Furthermore, we use magnetization mapping to show that the substituted atoms induce an overall magnetic moment in the graphene lattice, which may help guide the discussion on spintronic graphene. JTH, CBC, GH, and AVB acknowledge support from the Institute for Materials Science via the United States Basic Energy Sciences (E304).

Superfluid helium nanodroplets offer the opportunity to study dopant molecules in the sub-Kelvin range with only weak matrix perturbations. Femtosecond wave packet spectroscopy has been shown to be well suited to obtain high resolution vibrational spectra of cold alkali molecules in weakly bound high-spin states. In a pump-probe scheme a first laser pulse excites a vibrational wave packet that evolves on the molecular potential and is probed by a second ionizing pulse. We present spectroscopic data on Rb_3 and K_3 showing different vibronic progressions. These are assigned with the help of high level ab initio calculations of the electronic structure of the bare trimers. M. Mudrich, P. Heister, T. Hippler, C. Giese, O. Dulieu and F. Stienkemeier, Phys. Rev. A 80, 042512 (2009) J. Nagl, G. Auböck, A.W. Hauser, O. Allard, C. Callegari and W.E. Ernst, Phys. Rev. Lett. 100, 063001 (2008)

The vertebrate sodium (Nav) channel is composed of an ion-conducting α subunit and associated β subunits. Here, we report the crystal structure of the human β3 subunit immunoglobulin (Ig) domain, a functionally important component of Nav channels in neurons and cardiomyocytes. Surprisingly, we found that the β3 subunit Ig domain assembles as a trimer in the crystal asymmetric unit. Analytical ultracentrifugation confirmed the presence of Ig domain monomers, dimers, and trimers in free solution, and atomic force microscopy imaging also detected full-length β3 subunit monomers, dimers, and trimers. Mutation of a cysteine residue critical for maintaining the trimer interface destabilized both dimers and trimers. Using fluorescence photoactivated localization microscopy, we detected full-length β3 subunit trimers on the plasma membrane of transfected HEK293 cells. We further show that β3 subunits can bind to more than one site on the Nav 1.5 α subunit and induce the formation of α subunit oligomers, including trimers. Our results suggest a new and unexpected role for the β3 subunits in Nav channel cross-linking and provide new structural insights into some pathological Nav channel mutations. PMID:24567321

Ab initio computations at the MP2 level on five dimers and five cyclic trimers, drawn from water, ammonia, and formaldehyde are presented. Trimers have been drawn to present cyclic X-H---Y patterns. Particular attentions have been devoted in analyzing the energetic contributions resulting from cooperative effects in the trimer binding energies (BEs) and in analyzing the trends of several parameters from monomers to dimers and from dimers to trimers [in particular, the trends of the R(X-H) bond lengths, of the R(X---Y) distances, of the δvXH shifts in the vXH stretch vibrational frequencies, and of the electronic density ρc value at the XH---Y axis critical point when it exists]. The results have exhibited that cooperative effects represent from 10% to 16% of the trimer BEs and that they reinforce, from dimers to trimers, the trends observed for the above parameters from monomers to dimers. In particular, for "typical" X-H---Y HB (i.e., where X and Y atoms correspond to oxygen or nitrogen atoms), R(X-H) bond lengths are increased within 0.01 Å from monomers to dimers and from dimers to trimers, R(X---Y) distances shortened within 0.18 Å, ρc values increased by about 17% and vXH red-shifted from 18 to 164 cm-1 from dimers to trimers. As contrasted to those HBs the R(X-H) and δvXH parameters corresponding to C-H---Y interaction (with Y=O or N) follows an opposite trend from monomers to dimers and from dimers to trimers (i.e., they are respectively smoothly shortened and blue-shifted). All of these results therefore exhibit the great incidence of cooperative effects on the properties of X-H---Y interactions (corresponding to typical HBs or not), which are of importance to understand the properties of biochemical systems.

Tungsten W(111) oriented trimer-terminated tips as well as single atom tips, fabricated by a gas and field assisted etching and evaporation process, were investigated with a view to scanning ion microscopy and ion beam writing applications. In particular, ion current stability was studied for helium and neon imaging gases. Large ion current fluctuations from individual atomic sites were observed when a trimer-terminated tip was used for the creation of neon ion beam. However, neon ion current was stable when a single atom tip was employed. No such current oscillations were observed for either a trimer or a single atom tip when imaged with helium.

This paper reports on some preliminary experimental results of a work in progress regarding a problem involving the quantitative analysis of hydrogen isotopes by mass spectrometry of low resolution: the triatomic (trimer) ions interferences with the isotopic hydrogen species having the same mass/charge. These results indicate that, in complex mixtures of hydrogen isotopes, trimer ions are strongly affected by the presence of other species, and a new approach that takes into account the destruction mechanism of trimer ions is necessary for a proper determination of their contributions. PMID:23149602

Oligomeric and monomeric forms of chlorophyll-protein complexes of photosystem I (PSI) have been isolated from the mesophilic cyanobacterium Spirulina [(1992) FEBS Lett. 309, 340-342]. Electron microscopic analysis of the complexes showed that the oligomeric form is a trimer of the shape and dimensions similar to those of the trimer from thermophilic cyanobacteria. The chlorophyl ratio in the isolated trimer and monomer was found to be 7:3. The trimeric form of PSI complex in contrast to the monomeric one contains the chlorophyll emitting at 760 nm (77K), which is also found in Spirulina membranes and therefore could be used as an intrinsic probe for the trimeric complex. The 77K circular dichroism spectrum of the trimeric form is much more similar to that of Spirulina membranes than the spectrum of the monomer. Thus, the trimeric PSI complexes exist and dominate in the Spirulina membranes. PMID:8224233

We have investigated the immunogenicity in rabbits of native-like, soluble, recombinant SOSIP.664 trimers based on the env genes of four isolates of human immunodeficiency virus type 1 (HIV-1); specifically BG505 (clade A), B41 (clade B), CZA97 (clade C) and DU422 (clade C). The various trimers were delivered either simultaneously (as a mixture of clade A + B trimers) or sequentially over a 73-week period. Autologous, Tier-2 neutralizing antibody (NAb) responses were generated to the clade A and clade B trimers in the bivalent mixture. When delivered as boosting immunogens to rabbits immunized with the clade A and/or clade B trimers, the clade C trimers also generated autologous Tier-2 NAb responses, the CZA97 trimers doing so more strongly and consistently than the DU422 trimers. The clade C trimers also cross-boosted the pre-existing NAb responses to clade A and B trimers. We observed heterologous Tier-2 NAb responses albeit inconsistently, and with limited overall breath. However, cross-neutralization of the clade A BG505.T332N virus was consistently observed in rabbits immunized only with clade B trimers and then boosted with clade C trimers. The autologous NAbs induced by the BG505, B41 and CZA97 trimers predominantly recognized specific holes in the glycan shields of the cognate virus. The shared location of some of these holes may account for the observed cross-boosting effects and the heterologous neutralization of the BG505.T332N virus. These findings will guide the design of further experiments to determine whether and how multiple Env trimers can together induce more broadly neutralizing antibody responses. PMID:27627672

P2X2 receptor channel, a homotrimer activated by the binding of extracellular adenosine triphosphate (ATP) to three intersubunit ATP-binding sites (each located ∼50 Å from the ion permeation pore), also shows voltage-dependent activation upon hyperpolarization. Here, we used tandem trimeric constructs (TTCs) harboring critical mutations at the ATP-binding, linker, and pore regions to investigate how the ATP activation signal is transmitted within the trimer and how signals generated by ATP and hyperpolarization converge. Analysis of voltage- and [ATP]-dependent gating in these TTCs showed that: (a) Voltage- and [ATP]-dependent gating of P2X2 requires binding of at least two ATP molecules. (b) D315A mutation in the β-14 strand of the linker region connecting the ATP-binding domains to the pore-forming helices induces two different gating modes; this requires the presence of the D315A mutation in at least two subunits. (c) The T339S mutation in the pore domains of all three subunits abolishes the voltage dependence of P2X2 gating in saturating [ATP], making P2X2 equally active at all membrane potentials. Increasing the number of T339S mutations in the TTC results in gradual changes in the voltage dependence of gating from that of the wild-type channel, suggesting equal and independent contributions of the subunits at the pore level. (d) Voltage- and [ATP]-dependent gating in TTCs differs depending on the location of one D315A relative to one K308A that blocks the ATP binding and downstream signal transmission. (e) Voltage- and [ATP]-dependent gating does not depend on where one T339S is located relative to K308A (or D315A). Our results suggest that each intersubunit ATP-binding signal is directly transmitted on the same subunit to the level of D315 via the domain that contributes K308 to the β-14 strand. The signal subsequently spreads equally to all three subunits at the level of the pore, resulting in symmetric and independent contributions of the three

P2X2 receptor channel, a homotrimer activated by the binding of extracellular adenosine triphosphate (ATP) to three intersubunit ATP-binding sites (each located ∼50 Å from the ion permeation pore), also shows voltage-dependent activation upon hyperpolarization. Here, we used tandem trimeric constructs (TTCs) harboring critical mutations at the ATP-binding, linker, and pore regions to investigate how the ATP activation signal is transmitted within the trimer and how signals generated by ATP and hyperpolarization converge. Analysis of voltage- and [ATP]-dependent gating in these TTCs showed that: (a) Voltage- and [ATP]-dependent gating of P2X2 requires binding of at least two ATP molecules. (b) D315A mutation in the β-14 strand of the linker region connecting the ATP-binding domains to the pore-forming helices induces two different gating modes; this requires the presence of the D315A mutation in at least two subunits. (c) The T339S mutation in the pore domains of all three subunits abolishes the voltage dependence of P2X2 gating in saturating [ATP], making P2X2 equally active at all membrane potentials. Increasing the number of T339S mutations in the TTC results in gradual changes in the voltage dependence of gating from that of the wild-type channel, suggesting equal and independent contributions of the subunits at the pore level. (d) Voltage- and [ATP]-dependent gating in TTCs differs depending on the location of one D315A relative to one K308A that blocks the ATP binding and downstream signal transmission. (e) Voltage- and [ATP]-dependent gating does not depend on where one T339S is located relative to K308A (or D315A). Our results suggest that each intersubunit ATP-binding signal is directly transmitted on the same subunit to the level of D315 via the domain that contributes K308 to the β-14 strand. The signal subsequently spreads equally to all three subunits at the level of the pore, resulting in symmetric and independent contributions of the three

We discuss the use and importance of trimer-based systems because of the spin frustration that may arise within extended lattices comprised of trimers. The possible intra- and inter-trimer exchange pathways they posses due to interconnections are evaluated using density functional theory (DFT) to identify the optimal structures that may be used in designing extended lattices. As example, trinuclear Cu36+ cores with each pair of copper atoms bridged by carboxylate ligands have three-fold symmetry. As trimers these structures have the potential to be modeled as a frustrated quantum spin-1/2 system. To analyze the magnetic ground state and topological properties, we utilize exact diagonalization on small clusters and compare with Monte Carlo simulations for a range of system sizes. Research reported in this abstract was supported by UWF NIH MARC U-STAR 1T34GM110517-01.

A challenge for HIV-1 immunogen design is the difficulty of inducing neutralizing antibodies (NAbs) against neutralization-resistant (tier 2) viruses that dominate human transmissions. We show that a soluble recombinant HIV-1 envelope glycoprotein trimer that adopts a native conformation, BG505 SOSIP.664, induced NAbs potently against the sequence-matched tier 2 virus in rabbits and similar but weaker responses in macaques. The trimer also consistently induced cross-reactive NAbs against more sensitive (tier 1) viruses. Tier 2 NAbs recognized conformational epitopes that differed between animals and in some cases overlapped with those recognized by broadly neutralizing antibodies (bNAbs), whereas tier 1 responses targeted linear V3 epitopes. A second trimer, B41 SOSIP.664, also induced a strong autologous tier 2 NAb response in rabbits. Thus, native-like trimers represent a promising starting point for the development of HIV-1 vaccines aimed at inducing bNAbs. PMID:26089353

Trimers with one attractive bead and two repulsive beads, similar to recently synthesized trimer patchy colloids, were simulated with flat-histogram Monte Carlo methods to obtain the stable self-assembled structures for different shapes and interaction potentials. Extended corresponding states principle was successfully applied to self-assembling systems in order to approximately collapse the results for models with the same shape, but different interaction range. This helps us directly compare simulation results with previous experiment, and good agreement was found between the two. In addition, a variety of self-assembled structures were observed by varying the trimer geometry, including spherical clusters, elongated clusters, monolayers, and spherical shells. In conclusion, our results help to compare simulations and experiments, via extended corresponding states, and we predict the formation of self-assembled structures for trimer shapes that have not been experimentally synthesized. PMID:27087490

The ground state of a Cr trimer supported on the Au(111) surface is investigated by means of a variational approach to the Coqblin-Schrieffer Hamiltonian. The temperature of Kondo-resonance formation (T(K)) for equilateral trimers increases drastically as compared to T(K) for a single Cr adatom. The Kondo state of a Cr trimer proves to be very sensitive to geometry and a small shift of any atom from the symmetrical position leads to a rapid decrease in T(K). These results are in good agreement with recent observations of the Kondo response of a single antiferromagnetic chromium trimer [T. Jamneala, Phys. Rev. Lett. 87, 256804 (2001)

Immunization strategies that elicit antibodies capable of neutralizing diverse virus strains will likely be an important part of a successful vaccine against HIV. However, strategies to promote robust humoral responses against the native intact HIV envelope trimer structure are lacking. We recently developed chemically cross-linked lipid nanocapsules as carriers of molecular adjuvants and encapsulated or surface-displayed antigens, which promoted follicular helper T-cell responses and elicited high-avidity, durable antibody responses to a candidate malaria antigen. To apply this system to the delivery of HIV antigens, Env gp140 trimers with terminal his-tags (gp140T-his) were anchored to the surface of lipid nanocapsules via Ni-NTA-functionalized lipids. Initial experiments revealed that the large (409 kDa), heavily glycosylated trimers were capable of extracting fluid phase lipids from the membranes of nanocapsules. Thus, liquid-ordered and/or gel-phase lipid compositions were required to stably anchor trimers to the particle membranes. Trimer-loaded nanocapsules combined with the clinically relevant adjuvant monophosphoryl lipid A primed high-titer antibody responses in mice at antigen doses ranging from 5 μg to as low as 100 ng, whereas titers dropped more than 50-fold over the same dose range when soluble trimer was mixed with a strong oil-in-water adjuvant comparator. Nanocapsule immunization also broadened the number of distinct epitopes on the HIV trimer recognized by the antibody response. These results suggest that nanocapsules displaying HIV trimers in an oriented, multivalent presentation can promote key aspects of the humoral response against Env immunogens. PMID:25020048

Structures of BG505 SOSIP.664 trimer in complex with broadly neutralizing antibodies (bNAbs) have revealed the critical role of trimeric context for immune recognition of HIV-1. Presentation of trimeric HIV-1 antigens on nanoparticles may thus provide promising vaccine candidates. Here we report the rational design, structural analysis and antigenic evaluation of HIV-1 trimer-presenting nanoparticles. We first demonstrate that both V1V2 and gp120 can be presented in native-like trimeric conformations on nanoparticles. We then design nanoparticles presenting various forms of stabilized gp140 trimer based on ferritin and a large, 60-meric E2p that displays 20 spikes mimicking virus-like particles (VLPs). Particle assembly is confirmed by electron microscopy (EM), while antigenic profiles are generated using representative bNAbs and non-NAbs. Lastly, we demonstrate high-yield gp140 nanoparticle production and robust stimulation of B cells carrying cognate VRC01 receptors by gp120 and gp140 nanoparticles. Together, our study provides an arsenal of multivalent immunogens for HIV-1 vaccine development. PMID:27349934

Structures of BG505 SOSIP.664 trimer in complex with broadly neutralizing antibodies (bNAbs) have revealed the critical role of trimeric context for immune recognition of HIV-1. Presentation of trimeric HIV-1 antigens on nanoparticles may thus provide promising vaccine candidates. Here we report the rational design, structural analysis and antigenic evaluation of HIV-1 trimer-presenting nanoparticles. We first demonstrate that both V1V2 and gp120 can be presented in native-like trimeric conformations on nanoparticles. We then design nanoparticles presenting various forms of stabilized gp140 trimer based on ferritin and a large, 60-meric E2p that displays 20 spikes mimicking virus-like particles (VLPs). Particle assembly is confirmed by electron microscopy (EM), while antigenic profiles are generated using representative bNAbs and non-NAbs. Lastly, we demonstrate high-yield gp140 nanoparticle production and robust stimulation of B cells carrying cognate VRC01 receptors by gp120 and gp140 nanoparticles. Together, our study provides an arsenal of multivalent immunogens for HIV-1 vaccine development. PMID:27349934

HIV-1 enters target cells by virtue of envelope glycoprotein trimers that are incorporated at low density in the viral membrane. How many trimers are required to interact with target cell receptors to mediate virus entry, the HIV entry stoichiometry, still awaits clarification. Here, we provide estimates of the HIV entry stoichiometry utilizing a combined approach of experimental analyses and mathematical modeling. We demonstrate that divergent HIV strains differ in their stoichiometry of entry and require between 1 to 7 trimers, with most strains depending on 2 to 3 trimers to complete infection. Envelope modifications that perturb trimer structure lead to an increase in the entry stoichiometry, as did naturally occurring antibody or entry inhibitor escape mutations. Highlighting the physiological relevance of our findings, a high entry stoichiometry correlated with low virus infectivity and slow virus entry kinetics. The entry stoichiometry therefore directly influences HIV transmission, as trimer number requirements will dictate the infectivity of virus populations and efficacy of neutralizing antibodies. Thereby our results render consideration of stoichiometric concepts relevant for developing antibody-based vaccines and therapeutics against HIV. PMID:25569556

The HIV-1-envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a postfusion state. As the sole viral antigen on the HIV-1-virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5-Å resolution for an HIV-1-Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the prefusion conformation of gp41, indicates rearrangements needed for fusion activation, and defines parameters of immune evasion and immune recognition. Prefusion gp41 encircles N- and C-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry likely involve opening the clasp and expelling the termini. N-linked glycosylation and sequence-variable regions cover the prefusion closed spike: we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation. PMID:25296255

Disordered quantum networks, such as those describing light-harvesting complexes, are often characterized by the presence of peripheral ringlike structures, where the excitation is initialized, and inner structures and reaction centers (RCs), where the excitation is trapped and transferred. The peripheral rings often display distinguished coherent features: Their eigenstates can be separated, with respect to the transfer of excitation, into two classes of superradiant and subradiant states. Both are important to optimize transfer efficiency. In the absence of disorder, superradiant states have an enhanced coupling strength to the RC, while the subradiant ones are basically decoupled from it. Static on-site disorder induces a coupling between subradiant and superradiant states, thus creating an indirect coupling to the RC. The problem of finding the optimal transfer conditions, as a function of both the RC energy and the disorder strength, is very complex even in the simplest network, namely, a three-level system. In this paper we analyze such trimeric structure, choosing as the initial condition an excitation on a subradiant state, rather than the more common choice of an excitation localized on a single site. We show that, while the optimal disorder is of the order of the superradiant coupling, the optimal detuning between the initial state and the RC energy strongly depends on system parameters: When the superradiant coupling is much larger than the energy gap between the superradiant and the subradiant levels, optimal transfer occurs if the RC energy is at resonance with the subradiant initial state, whereas we find an optimal RC energy at resonance with a virtual dressed state when the superradiant coupling is smaller than or comparable to the gap. The presence of dynamical noise, which induces dephasing and decoherence, affects the resonance structure of energy transfer producing an additional incoherent resonance peak, which corresponds to the RC energy being

The trimeric envelope (Env) spike is the focus of vaccine design efforts aimed at generating broadly neutralizing antibodies (bNAbs) to protect against HIV-1 infection. Three recent developments have facilitated a thorough investigation of the antigenic structure of the Env trimer: 1) the isolation of many bNAbs against multiple different epitopes; 2) the generation of a soluble trimer mimic, BG505 SOSIP.664 gp140, that expresses most bNAb epitopes; 3) facile binding assays involving the oriented immobilization of tagged trimers. Using these tools, we generated an antigenic map of the trimer by antibody cross-competition. Our analysis delineates three well-defined epitope clusters (CD4 binding site, quaternary V1V2 and Asn332-centered oligomannose patch) and new epitopes at the gp120-gp41 interface. It also identifies the relationships among these clusters. In addition to epitope overlap, we defined three more ways in which antibodies can cross-compete: steric competition from binding to proximal but non-overlapping epitopes (e.g., PGT151 inhibition of 8ANC195 binding); allosteric inhibition (e.g., PGT145 inhibition of 1NC9, 8ANC195, PGT151 and CD4 binding); and competition by reorientation of glycans (e.g., PGT135 inhibition of CD4bs bNAbs, and CD4bs bNAb inhibition of 8ANC195). We further demonstrate that bNAb binding can be complex, often affecting several other areas of the trimer surface beyond the epitope. This extensive analysis of the antigenic structure and the epitope interrelationships of the Env trimer should aid in design of both bNAb-based therapies and vaccines intended to induce bNAbs. PMID:25807248

Styrene Acrylonitrile (SAN) Trimer is a by-product in the production of acrylonitrile styrene plastics. Following a report of a childhood cancer cluster in the Toms River section of Dover Township, New Jersey, SAN Trimer was identified as one of the groundwater contaminants at Reich Farm Superfund site in the township. The contaminants from the Reich Farm site’s ground water plume impacted two wells at the Parkway well field. The National Toxicology Program (NTP) studied the toxicity and carcinogenicity of SAN Trimer in rats exposed during their perinatal developmental period and adulthood. The chronic toxicity and carcinogenicity studies in F344/N rats were preceded by 7- and 18-week perinatal toxicity studies to determine the exposure concentrations for the 2-year studies. Subsequently, Fisher 344 pregnant dams were exposed to SAN Trimer containing diet at 400, 800, or 1600 ppm concentrations during gestation, nursing and weaning periods of offspring followed by two year of adult exposures to both male and female pups. There was no statistically significant evidence of carcinogenic activity following SAN-Trimer exposure; however, rare neoplasms in the brain and spinal cord were observed in males and to lesser extent in female rats. These incidences were considered within the range of historical background in the animal model used in the current studies. Therefore, the presence of a few rarely occurring CNS tumors in the treated groups were not judged to be associated with the SAN Trimer exposure. The major finding was a dose-related peripheral neuropathy associated with the sciatic nerves in females and spinal nerve roots in males and females thereby suggesting that SAN trimer is potentially a nervous system toxicant. PMID:24060431

HOX, PBX, and MEIS transcription factors bind DNA through a homeodomain. PBX proteins bind DNA cooperatively as heterodimers with MEIS family members and also with HOX proteins from paralog groups 1 to 10. MEIS proteins cooperatively bind DNA with ABD-B class HOX proteins of groups 9 and 10. Here, we examine aspects of dimeric and higher-order interactions between these three homeodomain classes. The most significant results can be summarized as follows. (i) Most of PBX N terminal to the homeodomain is required for efficient cooperative binding with HOXD4 and HOXD9. (ii) MEIS and PBX proteins form higher-order complexes on a heterodimeric binding site. (iii) Although MEIS does not cooperatively bind DNA with ANTP class HOX proteins, it does form a trimer as a non-DNA-binding partner with DNA-bound PBX-HOXD4. (iv) The N terminus of HOXD4 negatively regulates trimer formation. (v) MEIS forms a similar trimer with DNA-bound PBX-HOXD9. (vi) A related trimer (where MEIS is a non-DNA-binding partner) is formed on a transcriptional promoter within the cell. (vii) We observe an additional trimer class involving non-DNA-bound PBX and DNA-bound MEIS-HOXD9 or MEIS-HOXD10 heterodimers that is enhanced by mutation of the PBX homeodomain. (viii) In this latter trimer, PBX is likely to contact both MEIS and HOXD9/D10. (ix) The stability of DNA binding by all trimers is enhanced relative to the heterodimers. These findings suggest novel functions for PBX and MEIS in modulating the function of DNA-bound MEIS-HOX and PBX-HOX heterodimers, respectively. PMID:10523646

PG9 is the founder member of an expanding family of glycan-dependent human antibodies that preferentially bind the HIV (HIV-1) envelope (Env) glycoprotein (gp) trimer and broadly neutralize the virus. Here, we show that a soluble SOSIP.664 gp140 trimer constructed from the Clade A BG505 sequence binds PG9 with high affinity (∼11 nM), enabling structural and biophysical characterizations of the PG9:Env trimer complex. The BG505 SOSIP.664 gp140 trimer is remarkably stable as assessed by electron microscopy (EM) and differential scanning calorimetry. EM, small angle X-ray scattering, size exclusion chromatography with inline multiangle light scattering and isothermal titration calorimetry all indicate that only a single PG9 fragment antigen-binding (Fab) binds to the Env trimer. An ∼18 Å EM reconstruction demonstrates that PG9 recognizes the trimer asymmetrically at its apex via contact with two of the three gp120 protomers, possibly contributing to its reported preference for a quaternary epitope. Molecular modeling and isothermal titration calorimetry binding experiments with an engineered PG9 mutant suggest that, in addition to the N156 and N160 glycan interactions observed in crystal structures of PG9 with a scaffolded V1/V2 domain, PG9 makes secondary interactions with an N160 glycan from an adjacent gp120 protomer in the antibody-trimer complex. Together, these structural and biophysical findings should facilitate the design of HIV-1 immunogens that possess all elements of the quaternary PG9 epitope required to induce broadly neutralizing antibodies against this region. PMID:23426631

ABSTRACT The sequence diversity of human immunodeficiency virus type 1 (HIV-1) presents a formidable challenge to the generation of an HIV-1 vaccine. One strategy to address such sequence diversity and to improve the magnitude of neutralizing antibodies (NAbs) is to utilize multivalent mixtures of HIV-1 envelope (Env) immunogens. Here we report the generation and characterization of three novel, acute clade C HIV-1 Env gp140 trimers (459C, 405C, and 939C), each with unique antigenic properties. Among the single trimers tested, 459C elicited the most potent NAb responses in vaccinated guinea pigs. We evaluated the immunogenicity of various mixtures of clade C Env trimers and found that a quadrivalent cocktail of clade C trimers elicited a greater magnitude of NAbs against a panel of tier 1A and 1B viruses than any single clade C trimer alone, demonstrating that the mixture had an advantage over all individual components of the cocktail. These data suggest that vaccination with a mixture of clade C Env trimers represents a promising strategy to augment vaccine-elicited NAb responses. IMPORTANCE It is currently not known how to generate potent NAbs to the diverse circulating HIV-1 Envs by vaccination. One strategy to address this diversity is to utilize mixtures of different soluble HIV-1 envelope proteins. In this study, we generated and characterized three distinct, novel, acute clade C soluble trimers. We vaccinated guinea pigs with single trimers as well as mixtures of trimers, and we found that a mixture of four trimers elicited a greater magnitude of NAbs than any single trimer within the mixture. The results of this study suggest that further development of Env trimer cocktails is warranted. PMID:25540368

ABSTRACT Generating neutralizing antibodies (nAbs) is a major goal of many current HIV-1 vaccine efforts. To be of practical value, these nAbs must be both potent and cross-reactive in order to be capable of preventing the transmission of the highly diverse and generally neutralization resistant (Tier-2) HIV-1 strains that are in circulation. The HIV-1 envelope glycoprotein (Env) spike is the only target for nAbs. To explore whether Tier-2 nAbs can be induced by Env proteins, we immunized conventional mice with soluble BG505 SOSIP.664 trimers that mimic the native Env spike. Here, we report that it is extremely difficult for murine B cells to recognize the Env epitopes necessary for inducing Tier-2 nAbs. Thus, while trimer-immunized mice raised Env-binding IgG Abs and had high-quality T follicular helper (Tfh) cell and germinal center (GC) responses, they did not make BG505.T332N nAbs. Epitope mapping studies showed that Ab responses in mice were specific to areas near the base of the soluble trimer. These areas are not well shielded by glycans and likely are occluded on virions, which is consistent with the lack of BG505.T332N nAbs. These data inform immunogen design and suggest that it is useful to obscure nonneutralizing epitopes presented on the base of soluble Env trimers and that the glycan shield of well-formed HIV Env trimers is virtually impenetrable for murine B cell receptors (BCRs). IMPORTANCE Human HIV vaccine efficacy trials have not generated meaningful neutralizing antibodies to circulating HIV strains. One possible hindrance has been the lack of immunogens that properly mimic the native conformation of the HIV envelope trimer protein. Here, we tested the first generation of soluble, native-like envelope trimer immunogens in a conventional mouse model. We attempted to generate neutralizing antibodies to neutralization-resistant circulating HIV strains. Various vaccine strategies failed to induce neutralizing antibodies to a neutralization

ABSTRACT Major neutralizing antibody immune evasion strategies of the HIV-1 envelope glycoprotein (Env) trimer include conformational and structural instability. Stabilized soluble trimers such as BG505 SOSIP.664 mimic the structure of virion-associated Env but nevertheless sample different conformational states. Here we demonstrate that treating BG505 SOSIP.664 trimers with glutaraldehyde or a heterobifunctional cross-linker introduces additional stability with relatively modest effects on antigenicity. Thus, most broadly neutralizing antibody (bNAb) epitopes were preserved after cross-linking, whereas the binding of most weakly or nonneutralizing antibodies (non-NAb) was reduced. Cross-linking stabilized all Env conformers present within a mixed population, and individual conformers could be isolated by bNAb affinity chromatography. Both positive selection of cross-linked conformers using the quaternary epitope-specific bNAbs PGT145, PGT151, and 3BC315 and negative selection with non-NAbs against the V3 region enriched for trimer populations with improved antigenicity for bNAbs. Similar results were obtained using the clade B B41 SOSIP.664 trimer. The cross-linking method may, therefore, be useful for countering the natural conformational heterogeneity of some HIV-1 Env proteins and, by extrapolation, also vaccine immunogens from other pathogens. IMPORTANCE The development of a vaccine to induce protective antibodies against HIV-1 is of primary public health importance. Recent advances in immunogen design have provided soluble recombinant envelope glycoprotein trimers with near-native morphology and antigenicity. However, these trimers are conformationally flexible, potentially reducing B-cell recognition of neutralizing antibody epitopes. Here we show that chemical cross-linking increases trimer stability, reducing binding of nonneutralizing antibodies while largely maintaining neutralizing antibody binding. Cross-linking followed by positive or negative

A systematic investigation into the relationship between the solid-state luminescence and the intermolecular Au∙∙∙Au interactions in a series of pyrazolate-based gold(I) trimers; tris(μ2-pyrazolato-N,N')-tri-gold(I) (1), tris(μ2-3,4,5-trimethylpyrazolato-N,N')-tri-gold(I) (2), tris(μ2-3-methyl-5-phenylpyrazolato-N,N')-tri-gold(I) (3) and tris(μ2-3,5-diphenylpyrazolato-N,N')-tri-gold(I) (4) has been carried out using variable temperature and high pressure X-ray crystallography, solid-state emission spectroscopy, Raman spectroscopy and computational techniques. Single-crystal X-ray studies show that there is a significant reduction in the intertrimer Au∙∙∙Au distances both with decreasing temperature and increasing pressure. In the four complexes, the reduction in temperature from 293 to 100 K is accompanied by a reduction in the shortest intermolecular Au∙∙∙Au contacts of between 0.04 and 0.08 Å. The solid-state luminescent emission spectra of 1 and 2 display a red shift with decreasing temperature or increasing pressure. Compound 3 does not emit under ambient conditions but displays increasingly red-shifted luminescence upon cooling or compression. Compound 4 remains emissionless, consistent with the absence of intermolecular Au∙∙∙Au interactions. The largest pressure induced shift in emission is observed in 2 with a red shift of approximately 630 cm-1 per GPa between ambient and 3.80 GPa. The shifts in all the complexes can be correlated with changes in Au∙∙∙Au distance observed by diffraction.

A systematic investigation into the relationship between the solid-state luminescence and the intermolecular Au∙∙∙Au interactions in a series of pyrazolate-based gold(I) trimers; tris(μ2-pyrazolato-N,N')-tri-gold(I) (1), tris(μ2-3,4,5-trimethylpyrazolato-N,N')-tri-gold(I) (2), tris(μ2-3-methyl-5-phenylpyrazolato-N,N')-tri-gold(I) (3) and tris(μ2-3,5-diphenylpyrazolato-N,N')-tri-gold(I) (4) has been carried out using variable temperature and high pressure X-ray crystallography, solid-state emission spectroscopy, Raman spectroscopy and computational techniques. Single-crystal X-ray studies show that there is a significant reduction in the intertrimer Au∙∙∙Au distances both with decreasing temperature and increasing pressure. In the four complexes, the reduction in temperature from 293 to 100 K is accompanied by a reduction in the shortest intermolecular Au∙∙∙Au contacts of between 0.04more » and 0.08 Å. The solid-state luminescent emission spectra of 1 and 2 display a red shift with decreasing temperature or increasing pressure. Compound 3 does not emit under ambient conditions but displays increasingly red-shifted luminescence upon cooling or compression. Compound 4 remains emissionless, consistent with the absence of intermolecular Au∙∙∙Au interactions. The largest pressure induced shift in emission is observed in 2 with a red shift of approximately 630 cm-1 per GPa between ambient and 3.80 GPa. The shifts in all the complexes can be correlated with changes in Au∙∙∙Au distance observed by diffraction.« less

A systematic investigation into the relationship between the solid-state luminescence and the intermolecular Au⋅⋅⋅Au interactions in a series of pyrazolate-based gold(I) trimers; tris(μ2-pyrazolato-N,N′)-tri-gold(I) (1), tris(μ2-3,4,5- trimethylpyrazolato-N,N′)-tri-gold(I) (2), tris(μ2-3-methyl-5-phenylpyrazolato-N,N′)-tri-gold(I) (3) and tris(μ2-3,5-diphenylpyrazolato-N,N′)-tri-gold(I) (4) has been carried out using variable temperature and high pressure X-ray crystallography, solid-state emission spectroscopy, Raman spectroscopy and computational techniques. Single-crystal X-ray studies show that there is a significant reduction in the intertrimer Au⋅⋅⋅Au distances both with decreasing temperature and increasing pressure. In the four complexes, the reduction in temperature from 293 to 100 K is accompanied by a reduction in the shortest intermolecular Au⋅⋅⋅Au contacts of between 0.04 and 0.08 Å. The solid-state luminescent emission spectra of 1 and 2 display a red shift with decreasing temperature or increasing pressure. Compound 3 does not emit under ambient conditions but displays increasingly red-shifted luminescence upon cooling or compression. Compound 4 remains emissionless, consistent with the absence of intermolecular Au⋅⋅⋅Au interactions. The largest pressure induced shift in emission is observed in 2 with a red shift of approximately 630 cm−1 per GPa between ambient and 3.80 GPa. The shifts in all the complexes can be correlated with changes in Au⋅⋅⋅Au distance observed by diffraction. PMID:25331304

The titanium mediated trimerization of pyrazine leads to the formation of a tris-chelate complex employing a 4a,4b,8a,8b,12a,12b-hexahydrodiyprazino[2,3-f:2',3'-h]quinoxaline ligand (HATH6, 3). The driving force in the formation of the (Cp*2Ti)3(HATH6) complex 2 is attributed to the formation of six Ti-N bonds. We show that density functional theory (DFT) fails to predict quantitatively correct results. Therefore, post-Hartree-Fock methods, such as second-order Møller-Plesset perturbation theory (MP2), in combination with coupled-cluster (CC) methods must be used. Both MP2 and CCSD(T) levels of theory provide endothermic trimerization energies, showing that the plain pyrazine trimer is not stable with respect to decomposition into its monomers. Complete basis set (CBS) results for the MP2 level of theory were computed using explicitly correlated wave functions. With these, we estimate the CCSD(T) CBS limit of the hypothetical trimerization energy to be +0.78 eV. Thus, the trimerization is facilitated by the formation of six Ti-N bonds with a calculated formation energy of -1.32 eV per bond. PMID:26613146

The process of primary electric charge separation in photosynthesis takes place in the reaction centers, but photosynthesis can operate efficiently and fluently due to the activity of several pigment-protein complexes called antenna, which absorb light quanta and transfer electronic excitations toward the reaction centers. LHCII is the major photosynthetic pigment-protein antenna complex of plants and appears in the trimeric form. Several recent reports point to trimeric organization of LHCII as a key factor responsible for the chloroplast architecture via stabilization of granal organization of the thylakoid membranes. In the present work, we address the question of whether such an organization could also directly influence the antenna properties of this pigment-protein complex. Chlorophyll fluorescence analysis reveals that excitation energy transfer in LHCII is substantially more efficient in trimers and dissipative energy losses are higher in monomers. It could be concluded that trimers are exceptionally well suited to perform the antenna function. Possibility of fine regulation of the photosynthetic antenna function via the LHCII trimer-monomer transition is also discussed, based on the fluorescence lifetime analysis in a single chloroplast. PMID:26085037

Cocoa consumption is suggested to promote many health benefits, since cocoa is a rich source of flavanols; but amounts and profiles of flavanols depend strongly on the bean type, origin and manufacturing process. Roasting is known as a crucial step in technical treatment of cocoa, which leads to flavanol losses and modifications, especially the epimerization of (-)-epicatechin to (-)-catechin. This study monitors the influence of cocoa bean roasting on the composition of flavanol monomers to trimers, with special focus on epimerization, which was quantified for procyanidin dimers, and also observed for trimers for the first time. Five dimeric and two trimeric potential epimerization products were detected and the extent of epimerization during cocoa roasting was shown to be a function of temperature. The data also showed remarkable variations in the change of flavanol content. The quantified flavanols decreased about 50% in Java beans and increased about 30% in Ivory Coast beans, despite being roasted under equal conditions. PMID:23993533

Infrared spectra for matrix-isolated γ-butyrolactone and γ-butyrolactone-d_6 were obtained. The carbonyl stretching mode occurs at 1803 cm-1 for the monomer species, 1786 cm-1 for the dimer species, and 1774 cm-1 for the trimer species (1797, 1789 and 1770 cm-1 for the deuterated isotopomer.) Vibrational frequencies calculated using density functional theory are in agreement with the experimental values. Density functional theory was used to calculate the structures and binding energies of γ-butyrolactone dimers and trimers. Binding energies of 55-58 kJ mol-1 are predicted for the dimer structures. Optimized geometries for stacked and ring trimer structures have been calculated, with predicted binding energies of up to 68 kJ mol-1.

The majority of membrane proteins function as oligomers. However, it remains largely unclear how the oligomer stability of protein complexes correlates with their function. Understanding the relationship between oligomer stability and activity is essential to protein research and to virtually all cellular processes that depend on the function of protein complexes. Proteins make lasting or transient interactions as they perform their functions. Obligate oligomeric proteins exist and function exclusively at a specific oligomeric state. Although oligomerization is clearly critical for such proteins to function, a direct correlation between oligomer affinity and biological activity has not yet been reported. Here, we used an obligate trimeric membrane transporter protein, AcrB, as a model to investigate the correlation between its relative trimer affinity and efflux activity. AcrB is a component of the major multidrug efflux system in Escherichia coli. We created six AcrB constructs with mutations at the transmembrane intersubunit interface, and we determined their activities using both a drug susceptibility assay and an ethidium bromide accumulation assay. The relative trimer affinities of these mutants in detergent micelles were obtained using blue native polyacrylamide gel electrophoresis. A correlation between the relative trimer affinity and substrate efflux activity was observed, in which a threshold trimer stability was required to maintain efflux activity. The trimer affinity of the wild-type protein was approximately 3 kcal/mol more stable than the threshold value. Once the threshold was reached, an additional increase of stability in the range observed had no observable effect on protein activity. PMID:24854514

The four-component polypeptides of the 2-oxoacid dehydrogenase complex from the thermophilic archaeon Thermoplasma acidophilum assemble to give an active multienzyme complex possessing activity with the branched-chain 2-oxoacids derived from leucine, isoleucine and valine, and with pyruvate. The dihydrolipoyl acyl-transferase (E2) core of the complex is composed of identical trimer-forming units that assemble into a novel 42-mer structure comprising octahedral and icosahedral geometric aspects. From our previously determined structure of this catalytic core, the inter-trimer interactions involve a tyrosine residue near the C-terminus secured in a hydrophobic pocket of an adjacent trimer like a ball-and-socket joint. In the present study, we have deleted the five C-terminal amino acids of the E2 polypeptide (IIYEI) and shown by equilibrium centrifugation that it now only assembles into a trimeric enzyme. This was confirmed by SAXS analysis, although this technique showed the presence of approximately 20% hexamers. The crystal structure of the trimeric truncated E2 core has been determined and shown to be virtually identical with the ones observed in the 42-mer, demonstrating that removal of the C-terminal anchor does not significantly affect the individual monomer or trimer structures. The truncated E2 is still able to bind both 2-oxoacid decarboxylase (E1) and dihydrolipoamide dehydrogenase (E3) components to give an active complex with catalytic activity similar to the native multienzyme complex. This is the first report of an active mini-complex for this enzyme, and raises the question of why all 2-oxoacid dehydrogenase complexes assemble into such large structures. PMID:25088564

The insecticidal feature of the three-domain Cry δ-endotoxins from Bacillus thuringiensis is generally attributed to their capability to form oligomeric pores, causing lysis of target larval midgut cells. However, the molecular description of their oligomerization process has not been clearly defined. Here a stable prepore of the 65-kDa trypsin-activated Cry4Ba mosquito-specific toxin was established through membrane-mimetic environments by forming an ∼200-kDa octyl-β-d-glucoside micelle-induced trimer. The SDS-resistant trimer caused cytolysis to Sf9 insect cells expressing Aedes-mALP (a Cry4Ba receptor) and was more effective than a toxin monomer in membrane perturbation of calcein-loaded liposomes. A three-dimensional model of toxin trimer obtained by negative-stain EM in combination with single-particle reconstruction at ∼5 nm resolution showed a propeller-shaped structure with 3-fold symmetry. Fitting the three-dimensional reconstructed EM map with a 100-ns molecular dynamics-simulated Cry4Ba structure interacting with an octyl-β-d-glucoside micelle showed relative positioning of individual domains in the context of the trimeric complex with a major protrusion from the pore-forming domain. Moreover, high-speed atomic force microscopy imaging at nanometer resolution and a subsecond frame rate demonstrated conformational transitions from a propeller-like to a globularly shaped trimer upon lipid membrane interactions, implying prepore-to-pore conversion. Real-time trimeric arrangement of monomers associated with l-α-dimyristoylphosphatidylcholine/3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonic acid bicelle membranes was also envisaged by successive high-speed atomic force microscopy imaging, depicting interactions among three individual subunits toward trimer formation. Together, our data provide the first pivotal insights into the structural requirement of membrane-induced conformational changes of Cry4Ba toxin monomers for the

We study a structure composed of three coupled waveguides with gain and loss, a non-Hermitian trimer. We demonstrate that the mode spectrum can be entirely real if the waveguides are placed in a special order and at certain distances between each other. Such structures generally lack a spatial symmetry, in contrast to parity-time symmetric trimers which are known to feature a real spectrum. We also determine a threshold for wave amplification and analyse the scattering properties of such non-conservative systems embedded into a chain of conservative waveguides.

Summary Viral glycoproteins mediate entry by pH-activated or receptor-engaged activation and exist in metastable pre-fusogenic states that may be stabilized by directed rational design. As recently reported, the conformationally fixed HIV-1 envelope glycoprotein (Env) trimers in the pre-fusion state (SOSIP) display molecular homogeneity and structural integrity at relatively high levels of resolution. However, the SOSIPs necessitate full Env precursor cleavage, which requires endogenous furin over-expression. Here, we developed an alternative strategy using flexible peptide covalent linkage of Env subdomains to produce soluble, homogeneous and cleavage-independent Env mimics, called native flexibly linked (NFL) trimers, as vaccine candidates. This simplified design avoids the need for furin co-expression and, in one case, antibody affinity purification to accelerate trimer scale-up for preclinical and clinical applications. We have successfully translated the NFL design to multiple HIV-1 subtypes, establishing the potential to become a general method of producing native-like, well-ordered Env trimers for HIV-1 or other viruses. PMID:25892233

A series of substituted aliphatic nitriles have been trimerized to their corresponding pyrimidine structures under solvent-free conditions in the presence of catalytic quantities of potassium tert-butoxide using a focused microwave reactor. Multigram quantities of the corresponding 4-aminopyrimidines have been prepared in high yields and purity following a simple and scaleable protocol. PMID:15877477

All singly substituted {sup 13}C, {sup 18}O, and {sup 34}S isotopomers of the previously known OCS trimer are observed in natural abundance in a broad-band spectrum measured with a chirped-pulse Fourier transform microwave spectrometer. The complete substitution structure thus obtained critically tests (and confirms) the common assumption that monomers tend to retain their free structure in a weakly bound cluster. A new OCS trimer isomer is also observed, and its structure is determined to be barrel-shaped but with the monomers all approximately aligned, in contrast to the original trimer which is barrel-shaped with two monomers aligned and one anti-aligned. An OCS tetramer spectrum is assigned for the first time, and the tetramer structure resembles an original trimer with an OCS monomer added at the end with two sulfur atoms. Infrared spectra observed in the region of the OCS ν{sub 1} fundamental (≈2060 cm{sup −1}) are assigned to the same OCS tetramer, and another infrared band is tentatively assigned to a different tetramer isomer. The experimental results are compared and contrasted with theoretical predictions from the literature and from new cluster calculations which use an accurate OCS pair potential and assume pairwise additivity.

Fe(2)P-like structures can be strongly frustrated magnets due to their Kagome/triangular intercalated-layer structure. A complete magnetic solution of the complex spin architecture, and hence the full potential of the magnetic phenomena in Fe(2)P-like material prototypes, is yet to be found. A previous magnetic model for a representative FeCrAs-like system used a mean-field effective-spin to describe the 3g-Wyckoff located Fe-triangles. Such an approach demonstrated the outstanding magnetocaloric properties of the material but left the question of whether the intra-trimer interaction could lead to new physical phenomena and therefore more potentially useful properties. In this work Monte Carlo simulations are employed in order to understand both the influence of the additional degrees of freedom introduced by the Fe-trimers and the changes caused by all the possible exchange couplings between them. Complex scenarios arise, in which FM coupling in the trimers gives rise to both in-plane and out-of-plane inter-layer AFM states; whereas AFM exchange in the trimers gives rise to three distinct states, i.e. AFM-canted layers, a non-collinear superposition of ferromagnetic Kagome/triangular orderings, and tilted inter-planar AFM order. These last three configurations generate a double bifurcated magnetic phase diagram while the first one mimics the behavior seen in a model that treats the trimer as an effective-spin under an applied magnetic field. PMID:26125529

PDZ domains in general, and those of PSD-95 in particular, are emerging as promising drug targets for diseases such as ischemic stroke. We have previously shown that dimeric ligands that simultaneously target PDZ1 and PDZ2 of PSD-95 are highly potent inhibitors of PSD-95. However, PSD-95 and the related MAGUK proteins contain three consecutive PDZ domains, hence we envisioned that targeting all three PDZ domains simultaneously would lead to more potent and potentially more specific interactions with the MAGUK proteins. Here we describe the design, synthesis and characterization of a series of trimeric ligands targeting all three PDZ domains of PSD-95 and the related MAGUK proteins, PSD-93, SAP-97 and SAP-102. Using our dimeric ligands targeting the PDZ1-2 tandem as starting point, we designed novel trimeric ligands by introducing a PDZ3-binding peptide moiety via a cysteine-derivatized NPEG linker. The trimeric ligands generally displayed increased affinities compared to the dimeric ligands in fluorescence polarization binding experiments and optimized trimeric ligands showed low nanomolar inhibition towards the four MAGUK proteins, thus being the most potent inhibitors described. Kinetic experiments using stopped-flow spectrometry showed that the increase in affinity is caused by a decrease in the dissociation rate of the trimeric ligand as compared to the dimeric ligands, likely reflecting the lower probability of simultaneous dissociation of all three PDZ ligands. Thus, we have provided novel inhibitors of the MAGUK proteins with exceptionally high affinity, which can be used to further elucidate the therapeutic potential of these proteins. PMID:25658767

In a cellulose synthesis complex a "rosette" shape is responsible for the synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. Our work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer in solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. Moreover, the conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. Finally, this study strongly supports the "hexamer of trimers" model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product.

In a cellulose synthesis complex a "rosette" shape is responsible for the synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. Our work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer inmore » solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. Moreover, the conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. Finally, this study strongly supports the "hexamer of trimers" model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product.« less

We previously reported that an envelope (Env) glycoprotein immunogen (o-gp140{delta}V2SF162) containing a partial deletion in the second variable loop (V2) derived from the R5-tropic HIV-1 isolate SF162 partially protected vaccinated rhesus macaques against pathogenic SHIV{sub SF162P4} virus. Extending our studies to subtype C isolate TV1, we have purified o-gp140{delta}V2TV1 (subtype C {delta}V2 trimer) to homogeneity, performed glycosylation analysis, and determined its ability to bind CD4, as well as a panel of well-characterized neutralizing monoclonal antibodies (mAb). In general, critical epitopes are preserved on the subtype C {delta}V2 trimer; however, we did not observe significant binding for the b12 mAb. The molecular mass of subtype C {delta}V2 trimer was found to be 450 kDa, and the hydrodynamic radius was found to be 10.87 nm. Our data suggest that subtype C {delta}V2 trimer binds to CD4 with an affinity comparable to o-gp140{delta}V2SF162 (subtype B {delta}V2 trimer). Using isothermal titration calorimetric (ITC) analysis, we demonstrated that all three CD4 binding sites (CD4-BS) in both subtype C and B trimers are exposed and accessible. However, compared to subtype B trimer, the three CD4-BS in subtype C trimer have different affinities for CD4, suggesting a cooperativity of CD4 binding in subtype C trimer but not in subtype B trimer. Negative staining electron microscopy of the subtype C {delta}V2 trimer has demonstrated that it is in fact a trimer. These results highlight the importance of studying subtype C Env, and also of developing appropriate subtype C-specific reagents that may be used for better immunological characterization of subtype C Env for developing an AIDS vaccine.

HIV-1 envelope glycoproteins (Env) and Env-based immunogens usually do not interact efficiently with the inferred germline precursors of known broadly neutralizing antibodies (bNAbs). This deficiency may be one reason why Env and Env-based immunogens are not efficient at inducing bNAbs. We evaluated the binding of 15 inferred germline precursors of bNAbs directed to different epitope clusters to three soluble native-like SOSIP.664 Env trimers. We found that native-like SOSIP.664 trimers bind to some inferred germline precursors of bNAbs, particularly ones involving the V1/V2 loops at the apex of the trimer. The data imply that native-like SOSIP.664 trimers will be an appropriate platform for structure-guided design improvements intended to create immunogens able to target the germline precursors of bNAbs. PMID:26433050

A correlated many-body basis function is used to describe the {sup 4}He trimer and small helium clusters ({sup 4}He{sub N}) with N= 4 - 9. A realistic helium dimer potential is adopted. The ground state results of the {sup 4}He dimer and trimer are in close agreement with earlier findings. But no evidence is found for the existence of Efimov state in the trimer for the actual {sup 4}He-{sup 4}He interaction. However, decreasing the potential strength we calculate several excited states of the trimer which exhibit Efimov character. We also solve for excited state energies of these clusters which are in good agreement with Monte Carlo hyperspherical description.

We consider the ground state of a single ''spin-down'' impurity atom interacting attractively with a ''spin-up'' atomic Fermi gas. By constructing variational wave functions for polarons, molecules, and trimers, we perform a detailed study of the transitions between these dressed bound states as a function of mass ratio r=m{sub {up_arrow}}/m{sub {down_arrow}} and interaction strength. Crucially, we find that the presence of a Fermi sea enhances the stability of the p-wave trimer, which can be viewed as a Fulde-Ferrell-Larkin-Ovchinnikov molecule that has bound an additional majority atom. For sufficiently large r, we find that the transitions lie outside the region of phase separation of the imbalanced Fermi gas and should thus be observable in experiment, unlike the well-studied equal-mass case.

Bisphenol A (BPA) aggregates on Ag(111) shows a polymorphism between two supramolecular motifs leading to formation of distinct networks depending on thermal energy. With rising temperature a dimeric pairing scheme reversibly converts into a trimeric motif, which forms a hexagonal superstructure with complex dynamic characteristics. The trimeric arrangements notably organize spontaneously into a self-assembled one-component array with supramolecular BPA rotors embedded in a two-dimensional stator sublattice. By varying the temperature, the speed of the rotors can be controlled as monitored by direct visualization. A combination of scanning tunneling microscopy and dispersion-corrected density-functional tight-binding (DFTB-vdW(surf)) based molecular modeling reveals the exact atomistic position of each molecule within the assembly as well as the driving force for the formation of the supramolecular rotors. PMID:26849384

In this Letter we address the issue of how synthetic spin-orbit (SO) coupling can strongly affect three-body physics in ultracold atomic gases. We consider a system which consists of three fermionic atoms, including two spinless heavy atoms and one spin-1/2 light atom subjected to an isotropic SO coupling. We find that SO coupling can induce universal three-body bound states with a negative s-wave scattering length at a smaller mass ratio, where no trimer bound state can exist if in the absence of SO coupling. The energies of these trimers are independent of the high-energy cutoff, and therefore they are universal ones. Moreover, the resulting atom-dimer resonance can be effectively controlled by SO coupling strength. Our results can be applied to systems like a Li6 and K40 mixture.

Dark conglomerates of domains with opposite handedness, which are designated as dark conglomerate phases (DC phases), have attracted much attention. After designing an achiral liquid crystal trimer, 4,4′-bis{7-[4-(5-octyloxypyrimidin-2-yl)phenyloxy]heptyloxy}biphenyl (1), which exhibits only a nematic phase, we prepared binary mixtures with some typical rod-like nematic liquid crystals, i.e., 4′-hexyloxy-4-cyanobiphenyl (6OCB), 2-(4-hexyloxyphenyl)-5-pentyloxypyrimidine (PPY), or 4-methyloxyphenyl 4-hexyloxycyclohexanecarboxylate (PCA), and investigated their phase transition behaviour. The binary mixtures containing 55–90 mol% of 6OCB were found to exhibit a nematic phase and a DC phase of chiral domains with opposite handedness. However, neither PPY nor PCA induced such a chiral conglomerate phase in the mixture with trimer 1. We discuss how core–core interactions contribute to produce such a chiral conglomerate phase. PMID:26395546

ABSTRACT In hepatitis C virus (HCV)-infected cells, the envelope glycoproteins E1 and E2 assemble as a heterodimer. To investigate potential changes in the oligomerization of virion-associated envelope proteins, we performed SDS-PAGE under reducing conditions but without thermal denaturation. This revealed the presence of SDS-resistant trimers of E1 in the context of cell-cultured HCV (HCVcc) as well as in the context of HCV pseudoparticles (HCVpp). The formation of E1 trimers was found to depend on the coexpression of E2. To further understand the origin of E1 trimer formation, we coexpressed in bacteria the transmembrane (TM) domains of E1 (TME1) and E2 (TME2) fused to reporter proteins and analyzed the fusion proteins by SDS-PAGE and Western blotting. As expected for strongly interacting TM domains, TME1–TME2 heterodimers resistant to SDS were observed. These analyses also revealed homodimers and homotrimers of TME1, indicating that such complexes are stable species. The N-terminal segment of TME1 exhibits a highly conserved GxxxG sequence, a motif that is well documented to be involved in intramembrane protein-protein interactions. Single or double mutations of the glycine residues (Gly354 and Gly358) in this motif markedly decreased or abrogated the formation of TME1 homotrimers in bacteria, as well as homotrimers of E1 in both HCVpp and HCVcc systems. A concomitant loss of infectivity was observed, indicating that the trimeric form of E1 is essential for virus infectivity. Taken together, these results indicate that E1E2 heterodimers form trimers on HCV particles, and they support the hypothesis that E1 could be a fusion protein. IMPORTANCE HCV glycoproteins E1 and E2 play an essential role in virus entry into liver cells as well as in virion morphogenesis. In infected cells, these two proteins form a complex in which E2 interacts with cellular receptors, whereas the function of E1 remains poorly understood. However, recent structural data suggest that E1

The two-dimensional (2D) vibronic spectroscopy of molecular trimers is studied theoretically. The solution of the time-dependent Schrödinger equation is carried out with the multi-configurational time-dependent Hartree (MCTDH) method which allows for an efficient propagation of the multi-component wave functions. 2D-spectra are calculated for H- and J-type aggregates incorporating one or two vibrational modes for each monomer. In performing calculations for monomer, dimer, and trimer systems, it is documented how the vibronic structure of the 2D-spectrum changes upon aggregation. This is of importance for the characterization of aggregation behavior being influenced by experimental conditions such as temperature or concentration. PMID:27586920

The envelope glycoprotein trimer (Env) on the surface of HIV-1 recognizes CD4(+) T cells and mediates viral entry. During this process, Env undergoes substantial conformational rearrangements, making it difficult to study in its native state. Soluble stabilized trimers have provided valuable insights into the Env structure, but they lack the hydrophobic membrane proximal external region (MPER, an important target of broadly neutralizing antibodies), the transmembrane domain, and the cytoplasmic tail. Here we present (i) a cryogenic electron microscopy (cryo-EM) structure of a clade B virus Env, which lacks only the cytoplasmic tail and is stabilized by the broadly neutralizing antibody PGT151, at a resolution of 4.2 angstroms and (ii) a reconstruction of this form of Env in complex with PGT151 and MPER-targeting antibody 10E8 at a resolution of 8.8 angstroms. These structures provide new insights into the wild-type Env structure. PMID:26941313

The fluid phase diagram of trimer particles composed of one central attractive bead and two repulsive beads was determined as a function of simple geometric parameters using flat-histogram Monte Carlo methods. A variety of self-assembled structures were obtained including spherical micelle-like clusters, elongated clusters, and densely packed cylinders, depending on both the state conditions and shape of the trimer. Advanced simulation techniques were employed to determine transitions between self-assembled structures and macroscopic phases using thermodynamic and structural definitions. Simple changes in particle geometry yield dramatic changes in phase behavior, ranging from macroscopic fluid phase separation to molecular-scale self-assembly. In special cases, both self-assembled, elongated clusters and bulk fluid phase separation occur simultaneously. Our work suggests that tuning particle shape and interactions can yield superstructures with controlled architecture.

Spectroscopic studies of various atmospheres appearing in diamond film synthesis suggest evidence for carbon atoms, dimers, or trimers. Molecular dynamics simulations with the Brenner hydrocarbon potential are being used to investigate the elementary reactions of these species on a hydrogen-terminated diamond (111) surface. In principle these types of simulations can be extended to simulations of growth morphologies, in the 1-2 monolayer regime presently.

The tremendous pandemic potential of coronaviruses was demonstrated twice in the last decades by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the transmembrane spike glycoprotein S, which forms a trimer carrying receptor-binding and membrane fusion functions1. S also contains the principal antigenic determinants and is the target of neutralizing antibodies. Here we present the structure of a murine coronavirus S trimer ectodomain determined at 4.0 Å resolution by single particle cryo-electron microscopy. It reveals the metastable pre-fusion architecture of S and highlights key interactions stabilizing it. The structure shares a common core with paramyxovirus F proteins2,3, implicating mechanistic similarities and an evolutionary connection between these viral fusion proteins. The accessibility of the highly conserved fusion peptide at the periphery of the trimer indicates potential vaccinology strategies to elicit broadly neutralizing antibodies against coronaviruses. Finally, comparison with crystal structures of human coronavirus S domains allows rationalization of the molecular basis for species specificity based on the use of spatially contiguous but distinct domains. PMID:26855426

We measured the low energy electron stimulated desorption (ESD) of anions from thin films of native (TXT) and bromine monosubstituted (TBrXT) oligonucleotide trimers deposited on a gold surface (T = thymidine, X = T, deoxycytidine (C), deoxyadenosine (A) or deoxyguanosine (G), Br = bromine). The desorption of H{sup -}, CH{sub 3}{sup -}/NH{sup -}, O{sup -}/NH{sub 2}{sup -}, OH{sup -}, CN{sup -}, and Br{sup -} was induced by 0 to 20 eV electrons. Dissociative electron attachment, below 12 eV, and dipolar dissociation, above 12 eV, are responsible for the formation of these anions. The comparison of the results obtained for the native and brominated trimers suggests that the main pathways of TBrXT degradation correspond to the release of the hydride and bromide anions. Significantly, the presence of bromine in oligonucleotide trimers blocks the electron-induced degradation of nuclobases as evidenced by a dramatic decrease in CN{sup -} desorption. An increase in the yields of OH{sup -} is also observed. The debromination yield of particular oligonucleotides diminishes in the following order: BrdU > BrdA > BrdG > BrdC. Based on these results, 5-bromo-2{sup '}-deoxyuridine appears to be the best radiosensitizer among the studied bromonucleosides.

The tremendous pandemic potential of coronaviruses was demonstrated twice in the past few decades by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the transmembrane spike glycoprotein S, which forms a trimer carrying receptor-binding and membrane fusion functions. S also contains the principal antigenic determinants and is the target of neutralizing antibodies. Here we present the structure of a mouse coronavirus S trimer ectodomain determined at 4.0 Å resolution by single particle cryo-electron microscopy. It reveals the metastable pre-fusion architecture of S and highlights key interactions stabilizing it. The structure shares a common core with paramyxovirus F proteins, implicating mechanistic similarities and an evolutionary connection between these viral fusion proteins. The accessibility of the highly conserved fusion peptide at the periphery of the trimer indicates potential vaccinology strategies to elicit broadly neutralizing antibodies against coronaviruses. Finally, comparison with crystal structures of human coronavirus S domains allows rationalization of the molecular basis for species specificity based on the use of spatially contiguous but distinct domains. PMID:26855426

In this paper it is offered the simplest microscopic model for the description of the nanocomposite material, which is found under action of external electromagnetic (electric) field. At that, the trimer nanocluster embedded in the weakly structured non-dissipative matrix (for example, the polymeric, organic or amorphous types) is modeled as three- center molecular complex with one "excess" tunneling electron and all its centers are considered together with account of theirs ligand environment. The proposed model description is suitable to the trimer nanoclusters of bridge type, and to the nanotrimers such type in which the ions of 3d-metals and theirs oxides have the various oxidation degrees, and also to other three-center molecular complexes of similar types. For posed problem a description of external and internal factors and analysis of their interconnections are performed. Herewith, the given model is also characterized by fact that in addition to the explicit connections of its basic factors they, furthermore, are implicitly interconnected. Then, the mathematical model is formulated so that to contain an optimal number of model parameters for a detailed description of considered factors and its interconnections. In the result of numerical simulation can to identify the electron localization regimes in the trimer nanocluster and the values of controlling model parameters responsible for switching between the obtained regimes.

We measured the low energy electron stimulated desorption (ESD) of anions from thin films of native (TXT) and bromine monosubstituted (TBrXT) oligonucleotide trimers deposited on a gold surface (T = thymidine, X = T, deoxycytidine (C), deoxyadenosine (A) or deoxyguanosine (G), Br = bromine). The desorption of H-, CH3-/NH-, O-/NH2-, OH-, CN-, and Br- was induced by 0 to 20 eV electrons. Dissociative electron attachment, below 12 eV, and dipolar dissociation, above 12 eV, are responsible for the formation of these anions. The comparison of the results obtained for the native and brominated trimers suggests that the main pathways of TBrXT degradation correspond to the release of the hydride and bromide anions. Significantly, the presence of bromine in oligonucleotide trimers blocks the electron-induced degradation of nuclobases as evidenced by a dramatic decrease in CN- desorption. An increase in the yields of OH- is also observed. The debromination yield of particular oligonucleotides diminishes in the following order: BrdU > BrdA > BrdG > BrdC. Based on these results, 5-bromo-2'-deoxyuridine appears to be the best radiosensitizer among the studied bromonucleosides.

The outer membrane (OM) of gram-negative bacteria is an unusual asymmetric bilayer with an external monolayer of lipopolysaccharide (LPS) and an inner layer of phospholipids. The LPS layer is rigid and stabilized by divalent cation cross-links between phosphate groups on the core oligosaccharide regions. This means that the OM is robust and highly impermeable to toxins and antibiotics. During their biogenesis, OM proteins (OMPs), which function as transporters and receptors, must integrate into this ordered monolayer while preserving its impermeability. Here we reveal the specific interactions between the trimeric porins of Enterobacteriaceae and LPS. Isolated porins form complexes with variable numbers of LPS molecules, which are stabilized by calcium ions. In earlier studies, two high-affinity sites were predicted to contain groups of positively charged side chains. Mutation of these residues led to the loss of LPS binding and, in one site, also prevented trimerization of the porin, explaining the previously observed effect of LPS mutants on porin folding. The high-resolution X-ray crystal structure of a trimeric porin-LPS complex not only helps to explain the mutagenesis results but also reveals more complex, subtle porin-LPS interactions and a bridging calcium ion. PMID:27493217

Summary The HIV-1 envelope glycoprotein trimer is covered by an array of N-linked glycans that shield it from immune surveillance. The high density of glycans on the trimer surface imposes steric constraints limiting the actions of glycan-processing enzymes, so that multiple under-processed structures remain on specific areas. These oligomannose glycans are recognized by broadly neutralizing antibodies (bNAbs) that are not thwarted by the glycan shield but, paradoxically, target it. Our site-specific glycosylation analysis of a soluble, recombinant trimer (BG505 SOSIP.664) maps the extremes of simplicity and diversity of glycan processing at individual sites and reveals a mosaic of dense clusters of oligomannose glycans on the outer domain. Although individual sites usually minimally affect the global integrity of the glycan shield, we identify examples of how deleting some glycans can subtly influence neutralization by bNAbs that bind at distant sites. The network of bNAb-targeted glycans should be preserved on vaccine antigens. PMID:26972002

The external domains of the HIV-1 envelope glycoprotein (gp120 and the gp41 ectodomain, collectively known as gp140) contain all known viral neutralization epitopes. Various strategies have been used to create soluble trimers of the envelope to mimic the structure of the native viral protein, including mutation of the gp120-gp41 cleavage site, introduction of disulfide bonds, and fusion to heterologous trimerization motifs. We compared the effects on quaternary structure, antigenicity, and immunogenicity of three such motifs: T4 fibritin, a GCN4 variant, and the Escherichia coli aspartate transcarbamoylase catalytic subunit. Fusion of each motif to the C-terminus of a noncleavable JRCSF gp140(-) envelope protein led to enhanced trimerization but had limited effects on the antigenic profile and CD4-binding ability of the trimers. Immunization of rabbits provided no evidence that the trimerized gp140(-) constructs induced significantly improved neutralizing antibodies to several HIV-1 pseudoviruses, compared to gp140 lacking a trimerization motif. However, modest differences in both binding specificity and neutralizing antibody responses were observed among the various immunogens.

In order to study the effect of trimerization of proliferating cell nuclear antigen (PCNA) on its interaction with DNA polymerase (pol) delta and its loading onto DNA by replication factor C (RF-C) we have mutated a single tyrosine residue located at the subunit interface (Tyr114) to alanine. This mutation (Y114A) had a profound effect on PCNA, since it completely abolished trimer formation as seen by glycerol gradient sedimentation and native gel electrophoresis. Furthermore, the mutant protein was unable to stimulate DNA synthesis by pol delta and did not compete effectively with wild-type PCNA for pol delta, although it was able to oligomerize and could to some extent interact with subunits of functionally active PCNA. We thus conclude that PCNA molecules that are not part of a circular trimeric complex cannot interact with the pol delta core. furthermore, the mutant protein could not be loaded onto DNA by RF-C and did not compete with wild-type PCNA for loading onto DNA, indicating that PCNA trimerization may also be a prerequisite for its recognition by RF-C. The adverse effects caused by this single mutation suggest that trimerization of PCNA is essential for the monomers to keep their overall structure and that the structural changes imposed by trimerization are important for interaction with other proteins. Images PMID:8521831

Nipah virus (NiV) is a paramyxovirus that infects host cells through the coordinated efforts of two envelope glycoproteins. The G glycoprotein attaches to cell receptors, triggering the fusion (F) glycoprotein to execute membrane fusion. Here we report the first crystal structure of the pre-fusion form of the NiV-F glycoprotein ectodomain. Interestingly this structure also revealed a hexamer-of-trimers encircling a central axis. Electron tomography of Nipah virus-like particles supported the hexameric pre-fusion model, and biochemical analyses supported the hexamer-of-trimers F assembly in solution. Importantly, structure-assisted site-directed mutagenesis of the interfaces between F trimers highlighted the functional relevance of the hexameric assembly. Shown here, in both cell-cell fusion and virus-cell fusion systems, our results suggested that this hexamer-of-trimers assembly was important during fusion pore formation. We propose that this assembly would stabilize the pre-fusion F conformation prior to cell attachment and facilitate the coordinated transition to a post-fusion conformation of all six F trimers upon triggering of a single trimer. Together, our data reveal a novel and functional pre-fusion architecture of a paramyxoviral fusion glycoprotein. PMID:26646856

Bacterial chemoreceptors associate with the histidine kinase CheA and coupling protein CheW to form extended membrane arrays that receive and transduce environmental signals. A receptor trimers-of-dimers resides at each vertex of the hexagonal protein lattice. CheA is fully activated and regulated when it is integrated into the receptor assembly. To mimic these states in solution, we have engineered chemoreceptor cytoplasmic kinase-control modules (KCMs) based on the Escherichia coli aspartate receptor Tar that are covalently fused and trimerized by a foldon domain (TarFO). Small-angle X-ray scattering, multi-angle light scattering, and pulsed-dipolar electron spin resonance spectroscopy of spin-labeled proteins indicate that the TarFO modules assemble into homogeneous trimers wherein the protein interaction regions closely associate at the end opposite to the foldon domains. The TarFO variants greatly increase the saturation levels of phosphorylated CheA (CheA-P), indicating that the association with a trimer of receptor dimers changes the fraction of active kinase. However, the rate constants for CheA-P formation with the Tar variants are low compared to those for autophosphorylation by free CheA, and net phosphotransfer from CheA to CheY does not increase commensurately with CheA autophosphorylation. Thus, the Tar variants facilitate slow conversion to an active form of CheA that then undergoes stable autophosphorylation and is capable of subsequent phosphotransfer to CheY. Free CheA is largely incapable of phosphorylation but contains a small active fraction. Addition of TarFO to CheA promotes a planar conformation of the regulatory domains consistent with array models for the assembly state of the ternary complex and different from that observed with a single inhibitory receptor. Introduction of TarFO into E. coli cells activates endogenous CheA to produce increased clockwise flagellar rotation, with the effects increasing in the presence of the chemotaxis

Human immunodeficiency virus-1 (HIV-1) capsid protein (CA) has become a target of antiviral drug design in recent years. The recognition that binding of small molecules to the CA protein can result in the perturbation of capsid assembly or disassembly has led to mathematical modeling of the process. Although a number of capsid assembly models have been developed using biophysical parameters of the CA protein obtained experimentally, there is currently no model of CA polymerization that can be practically used to analyze in vitro CA polymerization data to facilitate drug discovery. Herein, we describe an equilibrium model of CA polymerization for the kinetic analysis of in vitro assembly of CA into polymer tubes. This new mathematical model has been used to assess whether a triangular trimer of dimers rather than a hexagonal hexamer can be the basic capsomere building block of CA polymer. The model allowed us to quantify for the first time the affinity for each of the four crucial interfaces involved in the polymerization process and indicated that the trimerization of CA dimers is a relatively slow step in CA polymerization in vitro. For wild-type CA, these four interfaces include the interface between two monomers of a CA dimer (K(D) = 6.6 μM), the interface between any two dimers within a CA trimer of dimers (K(D) = 32 nM), and two types of interfaces between neighboring trimers of dimers, either within the same ring around the perimeter of the polymer tube (K(D) = 438 nM) or from two adjacent rings (K(D) = 147 nM). A comparative analysis of the interface dissociation constants between wild-type and two mutant CA proteins, cross-linked hexamer (A14C/E45C/W184A/M185A) and A14C/E45C, yielded results that are consistent with the trimer of dimers with a triangular geometry being the capsomere building block involved in CA polymer growth. This work provides additional insights into the mechanism of HIV-1 CA assembly and may prove useful in elucidating how small

We have demonstrated electronic structure and magnetic properties of Cu{sub 3}, Ag{sub 3} and Au{sub 3} trimers using a full potential local orbital method in the framework of relativistic density functional theory. We have also shown that the non-relativistic generalized gradient approximation for the exchange-correlation energy functional gives reliable magnetic properties in coinage metal trimers compared to experiment. In addition we have indicated that the spin-orbit coupling changes the structure and magnetic properties of gold trimer while the structure and magnetic properties of copper and silver trimers are marginally affected. A significant orbital moment of 0.21μ{sub B} was found for most stable geometry of the gold trimer whereas orbital magnetism is almost quenched in the copper and silver trimers.

ABSTRACT We have investigated factors that influence the production of native-like soluble, recombinant trimers based on the env genes of two isolates of human immunodeficiency virus type 1 (HIV-1), specifically 92UG037.8 (clade A) and CZA97.012 (clade C). When the recombinant trimers based on the env genes of isolates 92UG037.8 and CZA97.012 were made according to the SOSIP.664 design and purified by affinity chromatography using broadly neutralizing antibodies (bNAbs) against quaternary epitopes (PGT145 and PGT151, respectively), the resulting trimers are highly stable and they are fully native-like when visualized by negative-stain electron microscopy. They also have a native-like (i.e., abundant) oligomannose glycan composition and display multiple bNAb epitopes while occluding those for nonneutralizing antibodies. In contrast, uncleaved, histidine-tagged Foldon (Fd) domain-containing gp140 proteins (gp140UNC-Fd-His), based on the same env genes, very rarely form native-like trimers, a finding that is consistent with their antigenic and biophysical properties and glycan composition. The addition of a 20-residue flexible linker (FL20) between the gp120 and gp41 ectodomain (gp41ECTO) subunits to make the uncleaved 92UG037.8 gp140-FL20 construct is not sufficient to create a native-like trimer, but a small percentage of native-like trimers were produced when an I559P substitution in gp41ECTO was also present. The further addition of a disulfide bond (SOS) to link the gp120 and gp41 subunits in the uncleaved gp140-FL20-SOSIP protein increases native-like trimer formation to ∼20 to 30%. Analysis of the disulfide bond content shows that misfolded gp120 subunits are abundant in uncleaved CZA97.012 gp140UNC-Fd-His proteins but very rare in native-like trimer populations. The design and stabilization method and the purification strategy are, therefore, all important influences on the quality of trimeric Env proteins and hence their suitability as vaccine components

Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing of the trimeric ebolavirus glycoprotein are described. The trimeric membrane-anchored ebolavirus envelope glycoprotein (GP) is responsible for viral attachment, fusion and entry. Knowledge of its structure is important both for understanding ebolavirus entry and for the development of medical interventions. Crystal structures of viral glycoproteins, especially those in their metastable prefusion oligomeric states, can be difficult to achieve given the challenges in production, purification, crystallization and diffraction that are inherent in the heavily glycosylated flexible nature of these types of proteins. The crystal structure of ebolavirus GP in its trimeric prefusion conformation in complex with a human antibody derived from a survivor of the 1995 Kikwit outbreak has now been determined [Lee et al. (2008 ▶), Nature (London), 454, 177–182]. Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing are described. Glycoproteins were produced in human embryonic kidney 293T cells, which allowed rapid screening of constructs and expression of protein in milligram quantities. Complexes of GP with an antibody fragment (Fab) promoted crystallization and a series of deglycosylation strategies, including sugar mutants, enzymatic deglycosylation, insect-cell expression and glycan anabolic pathway inhibitors, were attempted to improve the weakly diffracting glycoprotein crystals. The signal-to-noise ratio of the search model for molecular replacement was improved by determining the structure of the uncomplexed Fab. Phase combination with Fab model phases and a selenium anomalous signal, followed by NCS-averaged density modification, resulted in a clear interpretable electron-density map. Model building was assisted by the use of B-value-sharpened electron-density maps and the

Haemophilus biotype IV strains belonging to the recently recognized Haemophilus cryptic genospecies are an important cause of maternal genital tract and neonatal systemic infections and initiate infection by colonizing the genital or respiratory epithelium. To gain insight into the mechanism of Haemophilus cryptic genospecies colonization, we began by examining prototype strain 1595 and three other strains for adherence to genital and respiratory epithelial cell lines. Strain 1595 and two of the three other strains demonstrated efficient adherence to all of the cell lines tested. With a stably adherent variant of strain 1595, we generated a Mariner transposon library and identified 16 nonadherent mutants. All of these mutants lacked surface fibers and contained an insertion in the same open reading frame, which encodes a 157-kDa protein designated Cha for cryptic haemophilus adhesin. Analysis of the predicted amino acid sequence of Cha revealed the presence of an N-terminal signal peptide and a C-terminal domain bearing homology to YadA-like and Hia-like trimeric autotransporters. Examination of the C-terminal 120 amino acids of Cha demonstrated mobility as a trimer on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the capacity to present the passenger domain of the Hia trimeric autotransporter on the bacterial surface. Southern analysis revealed that the gene that encodes Cha is conserved among clinical isolates of the Haemophilus cryptic genospecies and is absent from the closely related species Haemophilus influenzae. We speculate that Cha is important in the pathogenesis of disease due to the Haemophilus cryptic genospecies and is in part responsible for the apparent tissue tropism of this organism. PMID:18424521

Paramyxovirus fusion (F) proteins promote membrane fusion between the viral envelope and host cell membranes, a critical early step in viral infection. Although mutational analyses have indicated that transmembrane (TM) domain residues can affect folding or function of viral fusion proteins, direct analysis of TM-TM interactions has proved challenging. To directly assess TM interactions, the oligomeric state of purified chimeric proteins containing the Staphylococcal nuclease (SN) protein linked to the TM segments from three paramyxovirus F proteins was analyzed by sedimentation equilibrium analysis in detergent and buffer conditions that allowed density matching. A monomer-trimer equilibrium best fit was found for all three SN-TM constructs tested, and similar fits were obtained with peptides corresponding to just the TM region of two different paramyxovirus F proteins. These findings demonstrate for the first time that class I viral fusion protein TM domains can self-associate as trimeric complexes in the absence of the rest of the protein. Glycine residues have been implicated in TM helix interactions, so the effect of mutations at Hendra F Gly-508 was assessed in the context of the whole F protein. Mutations G508I or G508L resulted in decreased cell surface expression of the fusogenic form, consistent with decreased stability of the prefusion form of the protein. Sedimentation equilibrium analysis of TM domains containing these mutations gave higher relative association constants, suggesting altered TM-TM interactions. Overall, these results suggest that trimeric TM interactions are important driving forces for protein folding, stability and membrane fusion promotion. PMID:24178297

With the recent improvements for chirped pulse FTMW (CP-FTMW) spectroscopy between 2-18 GHz, substitution structures of molecules and clusters with more than 10 heavy atoms are becoming routine. While previous CP-FTMW results for phenol dimer reported at this conference by Steber et al. necessitated reduced-band measurements in order to achieve the sensitivity to detect the carbon isotopologues, the latest improvements for the 2-8 GHz arrangement have enabled full band detection of all 12 ^{13}C and 2 ^{18}O isotopologues of phenol dimer in natural abundance, with improved fits for all detected species. In addition, the added sensitivity of this new 2-8 GHz configuration has enabled a full carbon substitution structure of phenol trimer. The experimental structure of phenol trimer, in agreement with the M06-2X/6-311++g(d,p) ab initio structure, is a C_{3} oblate symmetric top with 21 heavy atoms; however, all possible isotopic substitutions are off-symmetry axis, so the resulting detected isotopologues have been fit as c-type prolate asymmetric tops. Use of Kraitchman's equations for structural determination of a symmetric top molecule require some assumptions from the ab initio structure for the complete r_{s} structure of the trimer. A detailed summary of these methods, as well as the microwave results for both species, will be presented. A. L. Steber, J. L. Neill, D. P. Zaleski, B. H. Pate, A. Lesarri. 67th OSU Int. Symp. On Mol. Spectrosc., Columbus, OH, 2012, MH13.

It is not yet clear how bacterial outer membrane proteins reach their correct destination after they are secreted across the cytoplasmic membrane. We show here that porin OmpF is secreted into the medium as a water-soluble monomeric protein by spheroplasts of Escherichia coli. Furthermore, this monomeric porin is taken up by cell envelope preparations or purified lipopolysaccharides in the presence of 0.03% Triton X-100 and is converted correctly into the mature trimeric conformation. These results appear to reproduce a part of the physiological export and targeting steps of this protein. Images PMID:1689050

Low-temperature absorption, fluorescence, and persistent hole-burned spectra are reported for aggregates of the trimeric light-harvesting antenna complex of photosystem II (LHC II). The lowest energy Q{sub y}-state was found to lie at 681.5 nm on the basis of hole spectra, which corresponds to a 2 nm red shift relative to the isolated LHC II trimer. The electron phonon coupling of the 681.5 nm state is characterized by S {approximately} 0.8 and coupling to phonons with a mean frequency of {approximately} 20 cm{sup {minus}1} which is very similar to that of the isolated trimer. This coupling is consistent with the 4.2 K Stokes shift of the fluorescence originating from the 681.5 nm state. An adjacent state at 680.0 nm is assigned. On the basis of the results of Pieper et al. for the isolated trimer, a state at {approximately} 678.5 nm is inferred. These three lowest energy Q{sub y}-states are associated with the lowest energy chlorophyll a state of the subunit of the isolated LHC II trimer. Their degeneracy is removed because of structural heterogeneity. The hole-burning results indicate that, aside from a quite uniform and small red shifting, aggregation has little effect on the excitonic level structure and intrinsic dynamics of the isolated trimer. Take together, the results presented here and in Pieper et al. lead to a model that qualitatively accounts for the strong temperature dependence of aggregation-induced fluorescence quenching between 4.2 and 80 K.

To elucidate the time evolution of photo reaction of bacteriorhodopsin in glycerol mixed purple membrane at around 196 K under irradiation by red light, a kinetic model was constructed. The change of absorption with irradiation at times of 560 nm and 412 nm was analyzed for the purpose of determining reaction rates of photo reaction of bacteriorhodopsin and its product M intermediate. In this study it is shown that reaction rates of conversion from bacteriorhodopsin to the M intermediate can be explained by a set of linear differential equations. This model analysis concludes that bacteriorhodopsin in which constitutes a trimer unit with other two bacteriorhodopsin molecules changes into M intermediates in the 1.73 of reaction rate, in the initial step, and according to the number of M intermediate in a trimer unit, from three to one, the reaction rate of bacteriorhodopsin into M intermediates smaller as 1.73, 0.80, 0.19 which caused by influence of inter-molecular interaction between bacteriorhodopsin. PMID:27451646

Surfactant protein A (SP-A), one of four proteins associated with pulmonary surfactant, binds with high affinity to alveolar phospholipid membranes, positioning the protein at the first line of defense against inhaled pathogens. SP-A exhibits both calcium-dependent carbohydrate binding, a characteristic of the collectin family, and specific interactions with lipid membrane components. The crystal structure of the trimeric carbohydrate recognition domain and neck domain of SP-A was solved to 2.1-{angstrom} resolution with multiwavelength anomalous dispersion phasing from samarium. Two metalbinding sites were identified, one in the highly conserved lectin site and the other 8.5 {angstrom} away. The interdomain carbohydrate recognition domain-neck angle is significantly less in SP-A than in the homologous collectins, surfactant protein D, and mannose-binding protein. This conformational difference may endow the SP-A trimer with a more extensive hydrophobic surface capable of binding lipophilic membrane components. The appearance of this surface suggests a putative binding region for membrane-derived SP-A ligands such as phosphatidylcholine and lipid A, the endotoxic lipid component of bacterial lipopolysaccharide that mediates the potentially lethal effects of Gram-negative bacterial infection.

Epstein-Barr virus (EBV) is a herpesvirus that is associated with development of malignancies of lymphoid tissue. EBV infections are life-long and occur in >90% of the population. Herpesviruses enter host cells in a process that involves fusion of viral and cellular membranes. The fusion apparatus is comprised of envelope glycoprotein B (gB) and a heterodimeric complex made of glycoproteins H and L. Glycoprotein B is the most conserved envelope glycoprotein in human herpesviruses, and the structure of gB from Herpes simplex virus 1 (HSV-1) is available. Here, we report the crystal structure of the secreted EBV gB ectodomain, which forms 16-nm long spike-like trimers, structurally homologous to the postfusion trimers of the fusion protein G of vesicular stomatitis virus (VSV). Comparative structural analyses of EBV gB and VSV G, which has been solved in its pre and postfusion states, shed light on gB residues that may be involved in conformational changes and membrane fusion. Also, the EBV gB structure reveals that, despite the high sequence conservation of gB in herpesviruses, the relative orientations of individual domains, the surface charge distributions, and the structural details of EBV gB differ from the HSV-1 protein, indicating regions and residues that may have important roles in virus-specific entry.

Cyclophilin A (CyPA) is a cytosolic receptor of immunosuppressive drug cyclosporin A (CsA) which possesses peptidyl-prodyl cis/trans isomerase (PPIase) activity. The recombinant human CyPA (rhCyPA) gene has been expressed in E. coli M15. Purification was performed using salting-out, as well as Sephacryl S-100 and DEAE-Sepharose CL-6B column chromatography. The molecular weight is about 18 kDa, confirmed by SDS-PAGE and mass spectrum. The results of Native-PAGE and immunoblotting showed the existence of three bands, which agreed well with the gel filtration results. The molecular mass of the three bands determined via CTAB gel electrophoresis and SDS-PAGE (rhCyPA cross-linked with glutaraldehyde) was 18 kDa, 36 kDa and 54 kDa respectively. Further more, the native rhCyPA and the cross-linked rhCyPA had the similar chromatographic behavior in gel filtration. All of the evidences above suggest that rhCyPA exists in forms of monomer, dimer and trimer. Moreover, we observed that even at low protein concentrations CyPA largely occurs as a dimer in solution, and enzyme kinetic parameters showed that activity of dimer was much higher than monomer or trimer, which probably have some biological significances. PMID:21728990

A conventional solution-based route to a cyclic trimeric organozinc compound [{Zn(Et)(β-diketonate)}3] (β-diketonate=OC(OMe)CHC(Me)O, 1) is described, with 1 structurally characterized for the first time. The ligand selection of bidentate β-diketonates is shown to be key to isolating a cyclic trimer. Additional reaction of β-diketonates with diethyl zinc were spectroscopically characterized as compounds of the type [{Zn(Et)(β-diketonate)} n ] (β-diketonate=OC(Me)CHC(Me)O, 2, OC(OtBu)CHC(Me)O, 3). Further studies have shown that selective oxidation of these species produces cubanes of the general formula [{Zn(OC(R)CHC(Me)O)2Zn(Et)OEt}2] (R=OMe, 4; Me, 5; OtBu, 6), allowing a high oxygen content whilst remaining structurally suitable for use as precursors. The successful deposition of thin films of zinc oxide through aerosol-assisted chemical vapor deposition (AACVD), using a novel precursor, is described and fully characterized. PMID:27547637

Identification of mechanistically novel anti-HIV fusion inhibitors was accomplished using a computer-aided structure-based design approach with the goal of blocking the formation of the N-heptad repeat (NHR) trimer of the viral protein gp41. A virtual screening strategy that included per-residue interaction patterns (footprints) was employed to identify small molecules compatible with putative binding pockets at the internal interface of the NHR helices at the core native viral six-helix bundle. From a screen of ∼2.8 million compounds using the DOCK program, 120 with favorable energetic and footprint overlap characteristics were purchased and experimentally tested leading to two compounds with favorable cell-cell fusion (IC50) and cytotoxicity profiles. Importantly, both hits were identified on the basis of scores containing footprint overlap terms and would not have been identified using the standard DOCK energy function alone. To our knowledge, these compounds represent the first reported small molecules that inhibit viral entry via the proposed NHR-trimer obstruction mechanism. PMID:26013847

The oxidation of methane to methanol in methanotrophs is catalyzed by the enzyme methane monooxygenase (MMO). Two distinct forms of this enzyme exist, a soluble cytoplasmic MMO (sMMO) and a membrane-bound particulate form (pMMO). We describe here the biochemical characterization of a stable and active purified pMMO hydroxylase (pMMO-H) and report a three-dimensional (3D) structure, determined by electron microscopy and single-particle analysis at 23 A resolution. Both biochemical and structural data indicate that pMMO hydroxylase is trimeric, with each monomer unit comprised of three polypeptides of 47, 26, and 23 kDa. Comparison of the recent crystal structure [Lieberman, R. L., and Rosenzweig, A. C. (2005) Nature 434, 177] of an uncharacterized pMMO-H complex with the three-dimensional (3D) structure determined here yielded a good match between the principal features and the organization of the enzyme monomers into trimers. The data presented here advance our current understanding of particulate methane monooxygenase function by the characterization of an active form of the enzyme and the corresponding 3D structure. PMID:16101279

The acetylene trimerization on the group VIII transition metal atoms, Rh and Pd, as well as on Ag atoms supported on MgO thin films has been studied experimentally and theoretically. The three metal atoms with the atomic configurations 4d(8)5s1 (Rh), 4d10s0 (Pd) and 4d(10)5s1 (Ag) behave distinctly differently. The coinage metal atom silver is basically inert for this reaction, whereas Pd is active at 220 and 320 K, and Rh produces benzene in a rather broad temperature range from 350 to ca. 430 K. The origins of these differences are not only the different electronic configurations, leading to a weak interaction of acetylene with silver due to strong Pauli repulsion with the 5s electron but also the different stability and dynamics of the three atoms on the MgO surface. In particular, Rh and Pd atoms interact differently with surface defects like the oxygen vacancies (F centers) and the step edges. Pd atoms migrate already at low temperature exclusively to F centers where the cyclotrimerization is efficiently promoted. The Rh atoms on the other hand are not only trapped on F centers but also at step edges up to about 300 K. Interestingly, only Rh atoms on F centers catalyze the trimerization reaction whereas they are turned inert on the step edges due to strong steric effects. PMID:19791385

Tumor necrosis factor (TNF) is a homotrimeric cytokine that is a key mediator of inflammation. It is unstable at physiological concentrations and slowly converts into an inactive form. Here, we investigated the mechanism of this process by using a Förster resonance energy transfer (FRET) assay that allowed monitoring of monomeric subunit exchange in time. We observed continuous exchange of monomeric subunits even at concentrations of TNF high enough to maintain its bioactivity. The kinetics of this process closely corresponds with the appearance of monomeric subunits and disappearance of trimeric TNF in time at ng/ml concentrations as monitored by high-performance size-exclusion chromatography (HP-SEC). Furthermore, of the five therapeutic TNF inhibitors that are currently used in the clinic, three (adalimumab, infliximab, etanercept) were found to completely inhibit the monomer exchange reaction and stabilize TNF trimers, whereas golimumab and certolizumab could not prevent monomer exchange, but did slow down the exchange process. These differences were not correlated with the affinities of the TNF inhibitors, measured with both surface plasmon resonance (SPR) and in fluid phase using fluorescence-assisted HP-SEC. The stabilizing effect of these TNF inhibitors might result in prolonged residual TNF bioactivity under conditions of incomplete blocking, as observed in vitro for adalimumab. PMID:27605058

Oligonucleotides are structurally similar to short RNA strands. Therefore, their formation via non-enzymatic reactions is highly relevant to Gilbert's RNA world scenario (1986) and the origin of life. In laboratory synthesis of oligonucleotides from monomers, it is necessary to remove the water molecules from the reaction medium to shift the equilibrium in favor of oligonucleotide formation, which would have been impossible for reactions that took place in dilute solutions on the early Earth. Model studies designed to address this problem demonstrate that montmorillonite, a phyllosilicate common on Earth and identified on Mars, efficiently catalyzes phosphodiester-bond formation between activated mononucleotides in dilute solutions and produces RNA-like oligomers. The purpose of this study was to examine the sequences and regiospecificity of trimer isomers formed in the reaction of 5'-phosphorimidazolides of adenosine and uridine. Results demonstrated that regiospecificity and sequence specificity observed in the dimer fractions are conserved in their elongation products. With regard to regiospecificity, 61% of the linkages were found to be RNA-like 3',5'-phosphodiester bonds. With regard to sequence specificity, we found that 88% of the linear trimers were hetero-isomers with 61% A-monomer and 39% U-monomer incorporation. These results lend support to Bernal's hypothesis that minerals may have played a significant role in the chemical processes that led to the origin of life by catalyzing the formation of phosphodiester bonds in RNA-like oligomers.

Tumor necrosis factor (TNF) is a homotrimeric cytokine that is a key mediator of inflammation. It is unstable at physiological concentrations and slowly converts into an inactive form. Here, we investigated the mechanism of this process by using a Förster resonance energy transfer (FRET) assay that allowed monitoring of monomeric subunit exchange in time. We observed continuous exchange of monomeric subunits even at concentrations of TNF high enough to maintain its bioactivity. The kinetics of this process closely corresponds with the appearance of monomeric subunits and disappearance of trimeric TNF in time at ng/ml concentrations as monitored by high-performance size-exclusion chromatography (HP-SEC). Furthermore, of the five therapeutic TNF inhibitors that are currently used in the clinic, three (adalimumab, infliximab, etanercept) were found to completely inhibit the monomer exchange reaction and stabilize TNF trimers, whereas golimumab and certolizumab could not prevent monomer exchange, but did slow down the exchange process. These differences were not correlated with the affinities of the TNF inhibitors, measured with both surface plasmon resonance (SPR) and in fluid phase using fluorescence-assisted HP-SEC. The stabilizing effect of these TNF inhibitors might result in prolonged residual TNF bioactivity under conditions of incomplete blocking, as observed in vitro for adalimumab. PMID:27605058

The I100V isoform of toluene-4-monooxygenase was used to catalyze the oxidative polymerization of anthranil and various indoles under mildly acidic conditions, favoring the production of trimers. Compounds produced in sufficient yield were purified and tested for their ability to inhibit the growth of B. anthracis, E. faecalis, L. monocytogenes, S. aureus, and in some cases, F. tularensis. 15 of the compounds displayed promising antibacterial activity (MIC trimers were produced. One compound class produced was a group of substituted derivatives of the natural product 2,2-bis(3-indolyl) indoxyl. The other group of compounds identified was classified as tryptanthrin-like compounds, all having multi-ring pendant groups attached at position 11 of tryptanthrin. One compound of particular interest, SAB-J85, had a structure that suggests that any compound, with a ring structure that can be activated by an oxygenase, might serve as a substrate for combinatorial biocatalysis. PMID:26112315

Coiled coils are characteristic rope-like protein structures, constituted by one or more heptad repeats. Native coiled-coil structures play important roles in various biological processes, while the designed ones are widely employed in medicine and industry. To date, two major oligomeric states (i.e. dimeric and trimeric states) of a coiled-coil structure have been observed, plausibly exerting different biological functions. Therefore, exploration of the relationship between heptad repeat sequences and coiled coil structures is highly important. In this paper, we develop a new method named AAFreqCoil to classify parallel dimeric and trimeric coiled coils. Our method demonstrated its competitive performance when benchmarked based on 10-fold cross validation and jackknife cross validation. Meanwhile, the rules that can explicitly explain the prediction results of the test coiled coil can be extracted from the AAFreqCoil model for a better explanation of user predictions. A web server and stand-alone program implementing the AAFreqCoil algorithm are freely available at . PMID:25918905

In this paper we report the results of an extensive experimental kinetic study carried out on the novel ethylene trimerization catalyst system, comprising the chromium source [CrCl(3)(thf)(3)] (thf=tetrahydrofuran), a Ph(2)P-N(iPr)-P(Ph)-N(iPr)H (PNPNH) ligand (Ph=phenyl, iPr=isopropyl), and triethylaluminum (AlEt(3)) as activator. It could be shown that the initial activity shows a first-order dependency on the ethylene concentration. Also, a first-order dependency was found for the catalyst concentration. The initial activity follows a typical Arrhenius behavior with an experimentally determined activation energy of 52.6 kJ mol(-1). At elevated temperatures (ca. 80 degrees C), a significant deactivation was observed, which can be tentatively traced back to a ligand rearrangement in the presence of AlEt(3). After a fast initial phase, a pronounced 'kink' in the ethylene-uptake curve is observed, followed by a slow, almost linear, further increase of the total ethylene consumption. The catalyst composition, in particular the ligand/chromium and the cocatalyst/chromium molar ratio, has a strong impact on the catalytic performance of the trimerization of ethylene. PMID:20512824

The interaction of light with metal nanoparticles leads to novel phenomena mediated by surface plasmon excitations. In this paper we use single molecules to characterize the interaction of surface plasmons with light, and show that such interaction can strongly modulate the polarization of the emitted light. The simplest nanostructures that enable such polarization modulation are asymmetric silver nanocrystal trimers, where individual Raman scattering molecules are located in the gap between two of the nanoparticles. The third particle breaks the dipolar symmetry of the two-particle junction, generating a wavelength-dependent polarization pattern. Indeed, the scattered light becomes elliptically polarized and its intensity pattern is rotated in the presence of the third particle. We use a combination of spectroscopic observations on single molecules, scanning electron microscope imaging, and generalized Mie theory calculations to provide a full picture of the effect of particles on the polarization of the emitted light. Furthermore, our theoretical analysis allows us to show that the observed phenomenon is very sensitive to the size of the trimer particles and their relative position, suggesting future means for precise control of light polarization on the nanoscale.

HIV-1 envelope glycoproteins (Env) mediate viral entry into target cells and are essential to the infectious cycle. Understanding how those glycoproteins are able to fuel the fusion process through their conformational changes could lead to the design of better, more effective immunogens for vaccine strategies. Here we describe a cell-based ELISA assay that allows studying the recognition of trimeric HIV-1 Env by monoclonal antibodies. Following expression of HIV-1 trimeric Env at the surface of transfected cells, conformation specific anti-Env antibodies are incubated with the cells. A horseradish peroxidase-conjugated secondary antibody and a simple chemiluminescence reaction are then used to detect bound antibodies. This system is highly flexible and can detect Env conformational changes induced by soluble CD4 or cellular proteins. It requires minimal amount of material and no highly-specialized equipment or know-how. Thus, this technique can be established for medium to high throughput screening of antigens and antibodies, such as newly-isolated antibodies. PMID:25286159

Abstract A conventional solution‐based route to a cyclic trimeric organozinc compound [{Zn(Et)(β‐diketonate)}3] (β‐diketonate=OC(OMe)CHC(Me)O, 1) is described, with 1 structurally characterized for the first time. The ligand selection of bidentate β‐diketonates is shown to be key to isolating a cyclic trimer. Additional reaction of β‐diketonates with diethyl zinc were spectroscopically characterized as compounds of the type [{Zn(Et)(β‐diketonate)}n] (β‐diketonate=OC(Me)CHC(Me)O, 2, OC(OtBu)CHC(Me)O, 3). Further studies have shown that selective oxidation of these species produces cubanes of the general formula [{Zn(OC(R)CHC(Me)O)2Zn(Et)OEt}2] (R=OMe, 4; Me, 5; OtBu, 6), allowing a high oxygen content whilst remaining structurally suitable for use as precursors. The successful deposition of thin films of zinc oxide through aerosol‐assisted chemical vapor deposition (AACVD), using a novel precursor, is described and fully characterized. PMID:27547637

PG9 and PG16 are two quaternary-structure-specific broadly neutralizing antibodies with unique HCDR3 subdomains. Previously, we showed that glycosylphosphatidylinositol (GPI)-anchored HCDR3 subdomains (GPI-HCDR3) can be targeted to lipid rafts of the plasma membrane, bind to the epitope recognized by HCDR3 of PG16, and neutralize diverse HIV-1 isolates. In this study, we further developed trimeric GPI-HCDR3s and demonstrated that trimeric GPI-HCDR3 (PG16) dramatically improves anti-HIV-1 neutralization, suggesting that a stoichiometry of recognition of 3 or 2 HCDR3 molecules (PG16) to 1 viral spike is possible. PMID:23152526

In support of a deeper understanding of the chemistry of cyanoacetylene--a known constituent of planetary atmospheres and interstellar space--theoretical and experimental studies address the chemical mechanism of dimerization and trimerization, and provide high-resolution rotational spectra of two of the trimeric products, 1,2,3- and 1,2,4-tricyanobenzene. Analysis of the rotational spectra is particularly challenging because of quadrupolar coupling from three (14)N nuclei. The laboratory rotational spectra provide the basis for future searches for these polar aromatic compounds in interstellar space by radio astronomy. PMID:20967903

Summary The synthesis of star-shaped discotic liquid crystal trimers using Co2(CO)8-catalyzed terminal alkyne [2 + 2 + 2] cycloaddition reaction is reported. The trimers consist of three triphenylene discotic units linked to a central 1,2,4-trisubstituted benzene ring via flexible spacers. The trimers were synthesized in the yields up to 70% by mixing the monomers with 10 mol % of Co2(CO)8 as the catalyst in refluxing 1,4-dioxane. The liquid crystalline properties were investigated by using polarizing optical microscopy (POM), differential scanning calorimetry (DSC) and X-ray diffraction (XRD). Trimer 4 with an ester connecting group and a longer spacer exhibited a rectangular columnar mesophase, while 5b and 5c possessing an ether linkage and a shorter spacer display a hexagonal columnar mesophase. The connecting functional group and the length of the flexible spacer between the central benzene ring and the triphenylene units have pivotal influence on the mesomorphism. PMID:24367450

Clostridium botulinum produces a large toxin complex (L-TC) comprising botulinum neurotoxin associated with auxiliary nontoxic proteins. A complex of 33- and 17-kDa hemagglutinins (an HA-33/HA-17 trimer) enhances L-TC transport across the intestinal epithelial cell layer via binding HA-33 to a sugar on the cell surface. At least two subtypes of serotype C/D HA-33 exhibit differing preferences for the sugars sialic acid and galactose. Here, we compared the three-dimensional structures of the galactose-binding HA-33 and HA-33/HA-17 trimers produced by the C-Yoichi strain. Comparisons of serotype C/D HA-33 sequences reveal a variable region with relatively low sequence similarity across the C. botulinum strains; the variability of this region may influence the manner of sugar-recognition by HA-33. Crystal structures of sialic acid- and galactose-binding HA-33 are broadly similar in appearance. However, small-angle X-ray scattering revealed distinct solution structures for HA-33/HA-17 trimers. A structural change in the C-terminal variable region of HA-33 might cause a dramatic shift in the conformation and sugar-recognition mode of HA-33/HA-17 trimer. PMID:27237978

The structures of the phenol dimer and phenol trimer complexes in the gas phase have been determined using chirped-pulse Fourier transform microwave spectroscopy in the 2-8 GHz band. All fourteen (13)C and (18)O phenol dimer isotopologues were assigned in natural abundance. A full heavy atom experimental substitution structure was determined, and a least-squares fit ground state r0 structure was determined by proper constraint of the M06-2X/6-311++g(d,p) ab initio structure. The structure of phenol dimer features a water dimer-like hydrogen bond, as well as a cooperative contribution from inter-ring dispersion. Comparisons between the experimental structure and previously determined experimental structures, as well as ab initio structures from various levels of theory, are discussed. For phenol trimer, a C3 symmetric barrel-like structure is found, and an experimental substitution structure was determined via measurement of the six unique (13)C isotopologues. The least-squares fit rm((1)) structure reveals a similar interplay between hydrogen bonding and dispersion in the trimer, with water trimer-like hydrogen bonding and C-H···π interactions. PMID:23749053

Background HIV-1 is decorated with trimeric glycoprotein spikes that enable infection by engaging CD4 and a chemokine coreceptor, either CCR5 or CXCR4. The variable loop 3 (V3) of the HIV-1 envelope protein (Env) is the main determinant for coreceptor usage. The predominant CCR5 using (R5) HIV-1 Env has been intensively studied in function and structure, whereas the trimeric architecture of the less frequent, but more cytopathic CXCR4 using (X4) HIV-1 Env is largely unknown, as are the consequences of sequence changes in and near V3 on antigenicity and trimeric Env structure. Results Soluble trimeric gp140 Env constructs were used as immunogenic mimics of the native spikes to analyze their antigenic properties in the context of their overall 3D structure. We generated soluble, uncleaved, gp140 trimers from a prototypic T-cell line-adapted (TCLA) X4 HIV-1 strain (NL4-3) and a hybrid (NL4-3/ADA), in which the V3 spanning region was substituted with that from the primary R5 isolate ADA. Compared to an ADA (R5) gp140, the NL4-3 (X4) construct revealed an overall higher antibody accessibility, which was most pronounced for the CD4 binding site (CD4bs), but also observed for mAbs against CD4 induced (CD4i) epitopes and gp41 mAbs. V3 mAbs showed significant binding differences to the three constructs, which were refined by SPR analysis. Of interest, the NL4-3/ADA construct with the hybrid NL4-3/ADA CD4bs showed impaired CD4 and CD4bs mAb reactivity despite the presence of the essential elements of the CD4bs epitope. We obtained 3D reconstructions of the NL4-3 and the NL4-3/ADA gp140 trimers via electron microscopy and single particle analysis, which indicates that both constructs inherit a propeller-like architecture. The first 3D reconstruction of an Env construct from an X4 TCLA HIV-1 strain reveals an open conformation, in contrast to recently published more closed structures from R5 Env. Exchanging the X4 V3 spanning region for that of R5 ADA did not alter the open

The membrane-proximal external region (MPER) of gp41 is considered as a prime target for the induction of neutralizing antibodies, since it contains the epitopes for three broadly neutralizing antibodies (2F5, 4E10 and Z13). Here we present a novel gp41 construct (HA-gp41) comprising gp41 HR2 and MPER fused to two triple-stranded coiled-coil domains at both ends. HA-gp41 is trimeric, has a high helical content in solution and forms rod-like structures as revealed by negative staining electron microscopy. Immunization of rabbits with HA-gp41 induced antibodies directed against MPER, which failed to exert significant neutralization capacity against envelopes from primary isolates. Thus trimerisation of MPER regions does not suffice to induce a potent neutralizing antibody response specific for conserved regions within gp41.

The structural properties of helium triatomic systems are studied using hyperspherical coordinates. A slow variable discretization approach is adopted to solve the three-body Schrödinger equation, in which the Schrödinger equation in hyperangular coordinates is solved using basis splines at a series of fixed FEM-DVR (finite-element methods–discrete variable representation) hyperradii. We focus on studying the geometrical structure of the 4He3 and 3He4He2 triatomic systems. Using the bound state wave functions obtained, we calculate and analyze the one-dimensional pair distribution and angle distribution functions as well as the two-dimensional angle–angle distributions. All these bound states are found to exhibit such a floppy nature that classifying them into particular geometrical shapes does not appear to be sensible. A comparison will be made with some bound states of the neon trimer, which are expected to be more tightly bound.

Phthalocyanine (Pc) and porphyrin (Por) chromophores have been fused through the benzo[α]pyrazine moiety, resulting in unprecedented heteroleptic tetrapyrrole-fused dimers and trimers. The heteroleptic tetrapyrrole nature has been clearly revealed based on single-crystal X-ray diffraction analysis of the zinc dimer. Electrochemical analysis, theoretical calculations, and time-resolved spectroscopic results disclose that the two/three-tetrapyrrole-fused skeletons behave as one totally π-conjugated system as a result of the strong conjugative interaction between/among the tetrapyrrole chromophores. In particular, the effectively extended π-electron system through the fused-bridge induced strong electronic communication between the Pc and Por moieties and large transition dipole moments in the Pc-Por-fused systems, providing high fluorescence quantum yields (>0.13) and relatively long excited state lifetimes (>1.3 ns) in comparison with their homo-tetrapyrrole-fused analogues. PMID:26879243

Quantum chemical calculations have predicted the existence of a new carbon family with double-layered structures formed by arranging prism-C2n (n = 6, 8, and 12) units. Theoretical explorations of potential energy surfaces suggest the lowest barriers of the reaction channels to be ca. 30 kJ mol-1 for a D2h prism-C16 dimer and a D3h prism-C24 trimer. Geometry optimizations under periodic boundary conditions yield some prism-C2n sheets composed of CC single bonds of ca. 0.15-0.16 nm. The relative energies per one atom with respect to graphene are 90-160 kJ mol-1. Van der Waals thickness is estimated to be ca. 0.5 nm.

Small transition metal clusters at a high level of approximation i.e. including all the valence electrons in the calculation and also including extensive electron correlation were studied. Perhaps the most useful end result of these studies is the qualitative information about the electronic structure of these small metal clusters, including the nature of the bonding. The electronic structure studies of the small clusters are directly applicable to problems in catalysis. From comparison of dimers, trimers and possibly higher clusters, it is possible to extrapolate the information obtained to provide insights into the electronic structure of bulk transition metals and their interaction with other atoms and molecules at both surface and interior locations.

Small transition metal clusters were studied at a high level of approximation, including all the valence electrons in the calculation and extensive electron correlation, in order to understand the electronic structure of these small metal clusters. By comparison of dimers, trimers, and possibly higher clusters, the information obtained was used to provide insights into the electronic structure of bulk transition metals. Small metal clusters are currently of considerable experimental interest and some information is becomming available both from matrix electron spin resonance studies and from gas phase spectroscopy. Collaboration between theorists and experimentalists is thus expected to be especially profitable at this time since there is some experimental information which can serve to guide the theoretical work.

A new theoretical approach is presented for the general treatment of nonadiabatic hybrid dynamics (mixing classical and quantum approach) and applied to the postionization of rare-gas trimers. There was an important disagreement between trajectory surface hopping (TSH) or mean field (MF) approaches and the experimental results; noteworthy, with the new method qualitative and almost quantitative agreement is found for the fragmentation ratios of ionic monomers and dimers. For the first time in the theory as in the experiment, the dimers prevail for argon while monomers strongly dominate for the heavier rare gases, krypton and xenon. A new compromise between MF and TSH approaches is proposed and the new method is found quite robust with results not too sensitive to various possible implementations.

Poor pharmacokinetics and resistance within some tumor cell lines have been the major obstacles during the preclinical or clinical application of TRAIL (tumor-necrosis-factor (TNF)-related apoptosis-inducing ligand). The half-life of TRAIL114-281 (114 to 281 amino acids) was revealed to be no more than 30 minutes across species. Therefore maleimido activated PEG (polyethylene glycol) and MMAE (Monomethyl Auristatin E) were applied to site-specifically conjugate with the mutated cysteines from different monomers of TRAIL successively, taking advantage of steric effects involved within TRAIL mutant conjugations. As a result, TRAIL trimer was hetero-modified for different purposes. And the resulting PEG-TRAIL-vcMMAE conjugate exhibited dramatically improved half-life (11.54 h), favourable in vivo targeting capability and antitumor activities while no sign of toxicity in xenograft models, suggesting it’s a viable therapeutic and drug delivery strategy. PMID:26445897

Linker of nucleoskeleton and cytoskeleton (LINC) complexes span the nuclear envelope and are composed of KASH and SUN proteins residing in the outer and inner nuclear membrane, respectively. LINC formation relies on direct binding of KASH and SUN in the perinuclear space. Thereby, molecular tethers are formed that can transmit forces for chromosome movements, nuclear migration, and anchorage. We present crystal structures of the human SUN2-KASH1/2 complex, the core of the LINC complex. The SUN2 domain is rigidly attached to a trimeric coiled coil that prepositions it to bind three KASH peptides. The peptides bind in three deep and expansive grooves formed between adjacent SUN domains, effectively acting as molecular glue. In addition, a disulfide between conserved cysteines on SUN and KASH covalently links both proteins. The structure provides the basis of LINC complex formation and suggests a model for how LINC complexes might arrange into higher-order clusters to enhance force-coupling.

The cellular abundance of the cyclin-dependent kinase (Cdk) inhibitor p27 is regulated by the ubiquitin–proteasome system. Activation of p27 degradation is seen in proliferating cells and in many types of aggressive human carcinomas. p27 can be phosphorylated on threonine 187 by Cdks, and cyclin E/Cdk2 overexpression can stimulate the degradation of wild-type p27, but not of a threonine 187-to-alanine p27 mutant [p27(T187A)]. However, whether threonine 187 phosphorylation stimulates p27 degradation through the ubiquitin–proteasome system or an alternative pathway is still not known. Here, we demonstrate that p27 ubiquitination (as assayed in vivo and in an in vitro reconstituted system) is cell-cycle regulated and that Cdk activity is required for the in vitro ubiquitination of p27. Furthermore, ubiquitination of wild-type p27, but not of p27(T187A), can occur in G1-enriched extracts only upon addition of cyclin E/Cdk2 or cyclin A/Cdk2. Using a phosphothreonine 187 site-specific antibody for p27, we show that threonine 187 phosphorylation of p27 is also cell-cycle dependent, being present in proliferating cells but undetectable in G1 cells. Finally, we show that in addition to threonine 187 phosphorylation, efficient p27 ubiquitination requires formation of a trimeric complex with the cyclin and Cdk subunits. In fact, cyclin B/Cdk1 which can phosphorylate p27 efficiently, but cannot form a stable complex with it, is unable to stimulate p27 ubiquitination by G1 extracts. Furthermore, another p27 mutant [p27(CK−)] that can be phosphorylated by cyclin E/Cdk2 but cannot bind this kinase complex, is refractory to ubiquitination. Thus throughout the cell cycle, both phosphorylation and trimeric complex formation act as signals for the ubiquitination of a Cdk inhibitor. PMID:10323868

The henipaviruses, Hendra virus (HeV) and Nipah virus (NiV), are paramyxoviruses discovered in the mid- to late 1990s that possess a broad host tropism and are known to cause severe and often fatal disease in both humans and animals. HeV and NiV infect cells by a pH-independent membrane fusion mechanism facilitated by their attachment (G) and fusion (F) glycoproteins. Here, several soluble forms of henipavirus F (sF) were engineered and characterized. Recombinant sF was produced by deleting the transmembrane (TM) and cytoplasmic tail (CT) domains and appending a glycosylphosphatidylinositol (GPI) anchor signal sequence followed by GPI-phospholipase D digestion, appending a trimeric coiled-coil (GCNt) domain (sF(GCNt)), or deleting the TM, CT, and fusion peptide domain. These sF glycoproteins were produced as F(0) precursors, and all were apparent stable trimers recognized by NiV-specific antisera. Surprisingly, however, only the GCNt-appended constructs (sF(GCNt)) could elicit cross-reactive henipavirus-neutralizing antibody in mice. In addition, sF(GCNt) constructs could be triggered in vitro by protease cleavage and heat to transition from an apparent prefusion to postfusion conformation, transitioning through an intermediate that could be captured by a peptide corresponding to the C-terminal heptad repeat domain of F. The pre- and postfusion structures of sF(GCNt) and non-GCNt-appended sF could be revealed by electron microscopy and were distinguishable by F-specific monoclonal antibodies. These data suggest that only certain sF constructs could serve as potential subunit vaccine immunogens against henipaviruses and also establish important tools for further structural, functional, and diagnostic studies on these important emerging viruses. PMID:22915804

In the thylakoid membranes of the mesophilic cyanobacterium Synechocystis PCC6803, PSI reaction centers (RCs) are organized as monomers and trimers. PsaL, a 16 kDa hydrophobic protein, a subunit of the PSI RC, was previously identified as crucial for the formation of PSI trimers. In this work, the physiological effects accompanied by PSI oligomerization were studied using a PsaL-deficient mutant (ΔpsaL), not able to form PSI trimers, grown at various temperatures. We demonstrate that in wild-type Synechocystis, the monomer to trimer ratio depends on the growth temperature. The inactivation of the psaL gene in Synechocystis grown phototropically at 30°C induces profound morphological changes, including the accumulation of glycogen granules localized in the cytoplasm, resulting in the separation of particular thylakoid layers. The carotenoid composition in ΔpsaL shows that PSI monomerization leads to an increased accumulation of myxoxantophyll, zeaxanthin and echinenone irrespective of the temperature conditions. These xanthophylls are formed at the expense of β-carotene. The measured H2O→CO2 oxygen evolution rates in the ΔpsaL mutant are higher than those observed in the wild type, irrespective of the growth temperature. Moreover, circular dichroism spectroscopy in the visible range reveals that a peak attributable to long-wavelength-absorbing carotenoids is apparently enhanced in the trimer-accumulating wild-type cells. These results suggest that specific carotenoids are accompanied by the accumulation of PSI oligomers and play a role in the formation of PSI oligomer structure. PMID:25520404

The increased worldwide awareness of seasonal and pandemic influenza, including pandemic H1N1 virus, has stimulated interest in the development of economic platforms for rapid, large-scale production of safe and effective subunit vaccines. In recent years, plants have demonstrated their utility as such a platform and have been used to produce vaccine antigens against various infectious diseases. Previously, we have produced in our transient plant expression system a recombinant monomeric hemagglutinin (HA) protein (HAC1) derived from A/California/04/09 (H1N1) strain of influenza virus and demonstrated its immunogenicity and safety in animal models and human volunteers. In the current study, to mimic the authentic HA structure presented on the virus surface and to improve stability and immunogenicity of the HA antigen, we generated trimeric HA by introducing a trimerization motif from a heterologous protein into the HA sequence. Here, we describe the engineering, production in Nicotiana benthamiana plants, and characterization of the highly purified recombinant trimeric HA protein (tHA-BC) from A/California/04/09 (H1N1) strain of influenza virus. The results demonstrate the induction of serum hemagglutination inhibition antibodies by tHA-BC and its protective efficacy in mice against a lethal viral challenge. In addition, the immunogenic and protective doses of tHA-BC were much lower compared with monomeric HAC1. Further investigation into the optimum vaccine dose and/or regimen as well as the stability of trimerized HA is necessary to determine whether trimeric HA is a more potent vaccine antigen than monomeric HA. PMID:23296194

The structure of BG505 gp140 SOSIP, a soluble mimic of the native HIV-1 envelope glycoprotein (Env), marks the beginning of new era in Env structure-based immunogen design. Displaying a well-ordered quaternary structure, these subtype A-derived trimers display an excellent antigenic profile, discriminating recognition by broadly neutralizing antibodies (bNAbs) from non-broadly neutralizing antibodies (non-bNAbs), and provide a solid Env-based immunogenic platform starting point. Even with this important advance, obtaining homogeneous well-ordered soluble SOSIP trimers derived from other subtypes remains challenging. Here, we report the "rescue" of homogeneous well-ordered subtype B and C SOSIP trimers from a heterogeneous Env mixture using CD4 binding site-directed (CD4bs) non-bNAbs in a negative-selection purification process. These non-bNAbs recognize the primary receptor CD4bs only on disordered trimers but not on the native Env spike or well-ordered soluble trimers due to steric hindrance. Following negative selection to remove disordered oligomers, we demonstrated recovery of well-ordered, homogeneous trimers by electron microscopy (EM). We obtained 3D EM reconstructions of unliganded trimers, as well as in complex with sCD4, a panel of CD4bs-directed bNAbs, and the cleavage-dependent, trimer-specific bNAb, PGT151. Using bio-layer light interferometry (BLI) we demonstrated that the well-ordered trimers were efficiently recognized by bNAbs and poorly recognized by non-bNAbs, representing soluble mimics of the native viral spike. Biophysical characterization was consistent with the thermostability of a homogeneous species that could be further stabilized by specific bNAbs. This study revealed that Env trimers generate different frequencies of well-ordered versus disordered aberrant trimers even when they are genetically identical. By negatively selecting the native-like well-ordered trimers, we establish a new means to obtain soluble Env mimetics derived from

The structure of BG505 gp140 SOSIP, a soluble mimic of the native HIV-1 envelope glycoprotein (Env), marks the beginning of new era in Env structure-based immunogen design. Displaying a well-ordered quaternary structure, these subtype A-derived trimers display an excellent antigenic profile, discriminating recognition by broadly neutralizing antibodies (bNAbs) from non-broadly neutralizing antibodies (non-bNAbs), and provide a solid Env-based immunogenic platform starting point. Even with this important advance, obtaining homogeneous well-ordered soluble SOSIP trimers derived from other subtypes remains challenging. Here, we report the “rescue” of homogeneous well-ordered subtype B and C SOSIP trimers from a heterogeneous Env mixture using CD4 binding site-directed (CD4bs) non-bNAbs in a negative-selection purification process. These non-bNAbs recognize the primary receptor CD4bs only on disordered trimers but not on the native Env spike or well-ordered soluble trimers due to steric hindrance. Following negative selection to remove disordered oligomers, we demonstrated recovery of well-ordered, homogeneous trimers by electron microscopy (EM). We obtained 3D EM reconstructions of unliganded trimers, as well as in complex with sCD4, a panel of CD4bs-directed bNAbs, and the cleavage-dependent, trimer-specific bNAb, PGT151. Using bio-layer light interferometry (BLI) we demonstrated that the well-ordered trimers were efficiently recognized by bNAbs and poorly recognized by non-bNAbs, representing soluble mimics of the native viral spike. Biophysical characterization was consistent with the thermostability of a homogeneous species that could be further stabilized by specific bNAbs. This study revealed that Env trimers generate different frequencies of well-ordered versus disordered aberrant trimers even when they are genetically identical. By negatively selecting the native-like well-ordered trimers, we establish a new means to obtain soluble Env mimetics derived

Highlights: Black-Right-Pointing-Pointer ppGalNAc-T13 was up-regulated in high metastatic sublines of Lewis lung cancer. Black-Right-Pointing-Pointer ppGalNAc-T13 expression enhanced cell invasion activity in low metastatic sublines. Black-Right-Pointing-Pointer Trimeric Tn antigen was induced in the transfectant cells of ppGalNAc-T13 cDNA. Black-Right-Pointing-Pointer A major protein carrying trimeric Tn structure was identified as Syndecan-1. Black-Right-Pointing-Pointer Silencing of ppGalNAc-T13 resulted in the reduction of invasion and of metastasis.. -- Abstract: In order to analyze the mechanisms for cancer metastasis, high metastatic sublines (H7-A, H7-Lu, H7-O, C4-sc, and C4-ly) were obtained by repeated injection of mouse Lewis lung cancer sublines H7 and C4 into C57BL/6 mice. These sublines exhibited increased proliferation and invasion activity in vitro. Ganglioside profiles exhibited lower expression of GM1 in high metastatic sublines than the parent lines. Then, we established GM1-Si-1 and GM1-Si-2 by stable silencing of GM1 synthase in H7 cells. These GM1-knockdown clones exhibited increased proliferation and invasion. Then, we explored genes that markedly altered in the expression levels by DNA microarray in the combination of C4 vs. C4-ly or H7 vs. H7 (GM1-Si). Consequently, pp-GalNAc-T13 gene was identified as up-regulated genes in the high metastatic sublines. Stable transfection of pp-GalNAc-T13 cDNA into C4 (T13-TF) resulted in increased invasion and motility. Then, immunoblotting and flow cytometry using various antibodies and lectins were performed. Only anti-trimeric Tn antibody (mAb MLS128), showed increased expression levels of trimeric Tn antigen in T13-TF clones. Moreover, immunoprecipitation/immunoblotting was performed by mAb MLS128, leading to the identification of an 80 kDa band carrying trimeric Tn antigen, i.e. Syndecan-1. Stable silencing of endogenous pp-GalNAc-T13 in C4-sc (T13-KD) revealed that primary tumors generated by

We observed a photo-switching effect in [Cu{sup II}(1,4,8,11-tetraazacyclodecane)]{sub 2}[Mo{sup IV}(CN){sub 8}]{center_dot}10H{sub 2}O by irradiation with 410-nm light around room temperature using infrared spectroscopy. This photo-switching is caused by the photo-induced charge transfer from Mo{sup IV} to Cu{sup II}. The photo-induced phase thermally relaxed to the initial phase with a half-life time of 2.7 Multiplication-Sign 10{sup 1}, 6.9 Multiplication-Sign 10{sup 1}, and 1.7 Multiplication-Sign 10{sup 2} s at 293, 283, and 273 K, respectively. The relaxation process was analyzed using Hauser's equation, k=k{sub 0}exp[-(E{sub a}+E{sub a}{sup *}{gamma}) /k{sub B}T], where k is the rate constant of relaxation, k{sub 0} is the frequency factor, E{sub a} is the activation energy, E{sub a}{sup *} is the additional activation energy due to the cooperativity, and {gamma} is the fraction of the photo-induced phase. k{sub 0}, E{sub a}, and E{sub a}{sup *} were evaluated as 1.28 Multiplication-Sign 10{sup 7}{+-} 2.6 s{sup -1}, 4002 {+-} 188 cm{sup -1}, and 546 {+-} 318 cm{sup -1}, respectively. The value of E{sub a} is much larger than that of the relaxation process for the typical light-induced spin crossover effect (E{sub a} Almost-Equal-To 1000 cm{sup -1}). Room-temperature photo-switching is an important issue in the field of optical functional materials. The present system is useful for the demonstration of high-temperature photo-switching material.

Planar and nonplanar geometries of the keto-N9H and keto-N7H tautomers of the guanine base of DNA as well as the hydrogen bonded complexes of these species with three water molecules each were optimized using the density functional theory at the B3LYP/6-31G ∗ ∗ level. Geometries of the isolated bases were also optimized using the ab initio approach at the MP2/6-31G ∗ ∗ level. The isolated keto-N9H and keto-N7H tautomers as well as their hydrogen bonded complexes with three water molecules each were solvated in bulk water employing the polarized continuum model (PCM) of the self-consistent reaction field theory (SCRF). Stacked dimers and trimers of both the tautomers of guanine were generated by placing the planar forms of the species at a fixed distance of 3.5 Å from the neighboring one and rotating one molecule with respect to the other by 110° for the keto-N9H form and 90° for the keto-N7H form which corresponded to total energy minima at the B3LYP/6-31G ∗ ∗ level. Geometry optimization for the cation of the monomer of guanine was performed at the same level of theory, and its solvation in bulk water was treated using the PCM model of the SCRF theory. The geometries of complexes of the two tautomers of guanine with a Na + ion each were optimized at the B3LYP/6-31G ∗ ∗ level, and the Na + ion is predicted to bind with the keto-N9H tautomer preferentially. While the complex of the keto-N7H form of guanine with three water molecules in gas phase is slightly more stable than the corresponding complex of the keto-N9H form of guanine, the reverse is true in bulk water. Stacking interactions enhance the relative stability of the keto-N9H tautomer over that of the keto-N7H tautomer, suggesting that in bulk solutions, the former would be dominant. Electronic spectra of the isolated tautomers of guanine, those of their complexes with three water molecules each, the (keto-n9h and keto-n7h) cation of guanine, the complexes of the tautomers with a Na + ion

Three new ellagitannin monomers, nilotinins M5-M7 (1-3), a dimer, nilotinin D10 (4), and a trimer, nilotinin T1 (5), together with three known dimers, hirtellin D (7) and tamarixinins B (8) and C (9), and a trimer, hirtellin T2 (6), were isolated from Tamarix nilotica dried leaves. The structures of the tannins were elucidated by intensive spectroscopic methods and chemical conversions into known tannins. The new trimer (5) is a unique macrocyclic type whose monomeric units are linked together by an isodehydrodigalloyl and two dehydrodigalloyl moieties. Additionally, dimeric and trimeric macrocyclic-type tannins isolated from T. nilotica in this study were assessed for possible cytotoxic activity against four human tumor cell lines. Tumor-selective cytotoxicities of the tested compounds were higher than those of synthetic and natural potent cytotoxic compounds, including polyphenols, and comparable with those of 5-fluorouracil and melphalan. PMID:23675651

We provide the first experimental evidence for the excitation transfers between two trimers of an isolated C-phycocyanin hexamer (αβ) 6PCL RC27, at the end of the rod proximal to the core of PBS in cyanobacterium of Anabaena variabilis, with picosecond time-resolved fluorescence spectroscopy. Our results strongly suggest that the observed fluorescence decay constants around 20 and 10 ps time scales, shown in anisotropy decay, not in isotropic decay experiments arose from the excitation transfers between two trimers via two types of transfer pathways such as 1β 155↔6β 155 (2β 155↔5β 155 and 3β 155↔4β 155) and 2α 84↔5α 84 (3α 84↔6α 84 and 1α 84↔4α 84) channels and these could be described by Föster dipole-dipole resonance mechanism.

A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 envelope glycoprotein (Env). We previously demonstrated that a recombinant, soluble, fully cleaved SOSIP.664 trimer based on the clade A BG505 sequence is a faithful antigenic and structural mimic of the native trimer in its prefusion conformation. Here, we sought clade C native-like trimers with comparable properties. We identified DU422 and ZM197M SOSIP.664 trimers as being appropriately thermostable (Tm of 63.4 °C and 62.7 °C, respectively) and predominantly native-like, as determined by negative-stain electron microscopy (EM). Size exclusion chromatography, ELISA, and surface plasmon resonance further showed that these trimers properly display epitopes for all of the major bnAb classes, including quaternary-dependent, trimer-apex (e.g., PGT145) and gp120/gp41 interface (e.g., PGT151) epitopes. A cryo-EM reconstruction of the ZM197M SOSIP.664 trimer complexed with VRC01 Fab against the CD4 binding site at subnanometer resolution revealed a striking overall similarity to its BG505 counterpart with expected local conformational differences in the gp120 V1, V2, and V4 loops. These stable clade C trimers contribute additional diversity to the pool of native-like Env immunogens as key components of strategies to induce bnAbs to HIV-1. PMID:26372963

A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 envelope glycoprotein (Env). We previously demonstrated that a recombinant, soluble, fully cleaved SOSIP.664 trimer based on the clade A BG505 sequence is a faithful antigenic and structural mimic of the native trimer in its prefusion conformation. Here, we sought clade C native-like trimers with comparable properties. We identified DU422 and ZM197M SOSIP.664 trimers as being appropriately thermostable (Tm of 63.4 °C and 62.7 °C, respectively) and predominantly native-like, as determined by negative-stain electron microscopy (EM). Size exclusion chromatography, ELISA, and surface plasmon resonance further showed that these trimers properly display epitopes for all of the major bnAb classes, including quaternary-dependent, trimer-apex (e.g., PGT145) and gp120/gp41 interface (e.g., PGT151) epitopes. A cryo-EM reconstruction of the ZM197M SOSIP.664 trimer complexed with VRC01 Fab against the CD4 binding site at subnanometer resolution revealed a striking overall similarity to its BG505 counterpart with expected local conformational differences in the gp120 V1, V2, and V4 loops. These stable clade C trimers contribute additional diversity to the pool of native-like Env immunogens as key components of strategies to induce bnAbs to HIV-1. PMID:26372963

Dietary polyphenols exert neuroprotective effects in ischemic injury. The protective effects of a procyanidin type A trimer (trimer 1) isolated from a water soluble cinnamon extract (CE) were investigated on key features of ischemic injury, including cell swelling, increased free radical production, increased intracellular calcium ([Ca(2+)](i)), mitochondrial dysfunction, and the reduction in glutamate uptake. Astrocyte (glial) swelling is a major component of cytotoxic brain edema in ischemia and, along with vasogenic edema, may contribute to increased intracranial pressure, brain herniation, and additional ischemic injuries. C6 glial cultures were exposed to oxygen-glucose deprivation (OGD) for 5 h, and cell swelling was determined at 90 min after the end of OGD. OGD-induced increases in glial swelling were significantly blocked by trimer 1, but not by the major nonpolyphenol fractions of CE including cinnamaldehyde and coumarin. Increased free radical production, a contributing factor in cell swelling following ischemic injury, was also significantly reduced by trimer 1. Mitochondrial dysfunction, another key feature of ischemic injury, is hypothesized to contribute to glial swelling. Depolarization of the inner mitochondrial membrane potential (ΔΨ(m)) was assessed using a fluorescent dye (tetramethylrhodamine ethyl ester [TMRE]), and was significantly attenuated by trimer 1 as was OGD-induced increased [Ca(2+)](i). Taken together with our previous observation that blockers of [Ca(2+)](i) reduce cell swelling, our results indicate that trimer 1 may attenuate cell swelling by regulating [Ca(2+)](i). Trimer 1 also significantly attenuated the OGD-induced decrease in glutamate uptake. In addition, cyclosporin A, a blocker of the mitochondrial permeability pore (mPT), but not FK506 (that does not block the mPT), reduced the OGD-induced decline in glutamate uptake indicating a role of the mPT in such effects. Thus, the effects of trimer 1 in attenuating the

A desirable but as yet unachieved property of a human immunodeficiency virus type 1 (HIV-1) vaccine candidate is the ability to induce broadly neutralizing antibodies (bNAbs). One approach to the problem is to create trimeric mimics of the native envelope glycoprotein (Env) spike that expose as many bNAb epitopes as possible, while occluding those for non-neutralizing antibodies (non-NAbs). Here, we describe the design and properties of soluble, cleaved SOSIP.664 gp140 trimers based on the subtype A transmitted/founder strain, BG505. These trimers are highly stable, more so even than the corresponding gp120 monomer, as judged by differential scanning calorimetry. They are also homogenous and closely resemble native virus spikes when visualized by negative stain electron microscopy (EM). We used several techniques, including ELISA and surface plasmon resonance (SPR), to determine the relationship between the ability of monoclonal antibodies (MAbs) to bind the soluble trimers and neutralize the corresponding virus. In general, the concordance was excellent, in that virtually all bNAbs against multiple neutralizing epitopes on HIV-1 Env were highly reactive with the BG505 SOSIP.664 gp140 trimers, including quaternary epitopes (CH01, PG9, PG16 and PGT145). Conversely, non-NAbs to the CD4-binding site, CD4-induced epitopes or gp41ECTO did not react with the trimers, even when their epitopes were present on simpler forms of Env (e.g. gp120 monomers or dissociated gp41 subunits). Three non-neutralizing MAbs to V3 epitopes did, however, react strongly with the trimers but only by ELISA, and not at all by SPR and to only a limited extent by EM. These new soluble trimers are useful for structural studies and are being assessed for their performance as immunogens. PMID:24068931

The pathways and dynamics of excitation energy transfer between the chlorophyll (Chl) domains in solubilized trimeric and aggregated light-harvesting complex II (LHCII) are examined using two-dimensional electronic spectroscopy (2DES). The LHCII trimers and aggregates exhibit the unquenched and quenched excitonic states of Chl a, respectively. 2DES allows direct correlation of excitation and emission energies of coupled states over population time delays, hence enabling mapping of the energy flow between Chls. By the excitation of the entire Chl b Q{sub y} band, energy transfer from Chl b to Chl a states is monitored in the LHCII trimers and aggregates. Global analysis of the two-dimensional (2D) spectra reveals that energy transfer from Chl b to Chl a occurs on fast and slow time scales of 240–270 fs and 2.8 ps for both forms of LHCII. 2D decay-associated spectra resulting from the global analysis identify the correlation between Chl states involved in the energy transfer and decay at a given lifetime. The contribution of singlet–singlet annihilation on the kinetics of Chl energy transfer and decay is also modelled and discussed. The results show a marked change in the energy transfer kinetics in the time range of a few picoseconds. Owing to slow energy equilibration processes, long-lived intermediate Chl a states are present in solubilized trimers, while in aggregates, the population decay of these excited states is significantly accelerated, suggesting that, overall, the energy transfer within the LHCII complexes is faster in the aggregated state.

Linear optical spectra of solubilized trimers and small lamellar aggregates of the major light-harvesting complex II (LHCII) of higher plants are simulated employing excitonic couplings and site energies of chlorophylls (Chls) computed on the basis of the two crystal structures by a combined quantum chemical/electrostatic approach. A good agreement between simulation and experiment is achieved (except for the circular dichroism in the Chl b region), if vibronic transitions of Chls are taken into account. Site energies are further optimized by refinement fits of optical spectra. The differences between refined and directly calculated values are not significant enough to decide, whether the crystal structures are closer to trimers or aggregates. Changes in the linear dichroism spectrum upon aggregation are related to site energy shifts of Chls b601, b607, a603, a610, and a613, and are interpreted in terms of conformational changes of violaxanthin and the two luteins involving their ionone rings. Chl a610 is the energy sink at 77K in both conformations. An analysis of absorption spectra of trimers perpendicular and parallel to the C(3)-axis (van Amerongen et al. Biophys. J. 67 (1994) 837-847) shows that only Chl a604 close to neoxanthin is significantly reoriented in trimers compared to the crystal structures. Whether this pigment is orientated in aggregates as in the crystal structures, can presently not be determined faithfully. To finally decide about pigment reorientations that could be of relevance for non-photochemical quenching, further polarized absorption and fluorescence measurements of aggregates or detergent-depleted LHCII would be helpful. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial. PMID:22387396

Gene product 12 of bacteriophage T4, adhesin, serves to adhere the virus to host cells. Adhesin is a fibrous homotrimer, and a novel tertiary structure element, a beta-helix, is supposed to be a major structural feature of this protein. We have constructed two truncated gp12 mutants, 12N1 and 12N2, containing 221 and 135 N-terminal residues, respectively. When expressed in E. coli cells, these gp12 fragments formed labile beta-structural trimers. Another hybrid protein, 12FN, containing 179 N-terminal amino acid residues of gp12 fused to the C-terminal domain (31 amino acids) of T4 fibritin, was shown to have a trimeric proteolytically resistant alpha-helical structure. This structure is probably similar to that of fibritin, which has a triple alpha-helical coiled-coil structure. Hence, we have demonstrated the possibility of global transformation of fibrous protein structure using fusion with a C-terminal domain that initiates trimerization. PMID:11173503

ABSTRACT Next-generation sequencing (NGS) has been used to investigate the diversity and maturation of broadly neutralizing antibodies (bNAbs) in HIV-1-infected individuals. However, the application of NGS to the preclinical assessment of human vaccines, particularly the monitoring of vaccine-induced B-cell responses in a nonhuman primate (NHP) model, has not been reported. Here, we present a longitudinal NGS analysis of memory B-cell responses to an HIV-1 trimer vaccine in a macaque that has been extensively studied by single B-cell sorting and antibody characterization. We first established an NHP antibodyomics pipeline using the available 454 pyrosequencing data from this macaque and developed a protocol to sequence the NHP antibody repertoire in an unbiased manner. Using these methods, we then analyzed memory B-cell repertoires at four time points of NHP immunization and traced the lineages of seven CD4-binding site (CD4bs)-directed monoclonal antibodies previously isolated from this macaque. Longitudinal analysis revealed distinct patterns of B-cell lineage development in response to an HIV-1 trimer vaccine. While the temporal B-cell repertoire profiles and lineage patterns provide a baseline for comparison with forthcoming HIV-1 trimer vaccines, the newly developed NHP antibody NGS technologies and antibodyomics tools will facilitate future evaluation of human vaccine candidates. PMID:26530382

Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous metal-ion-extracting reagents, is an important ligand used in solvent extraction processes for the recovery of uranium and plutonium from spent nuclear fuel, as well as other non-nuclear applications. Ligand-ligand and organic solvent-ligand interactions play an important role in these processes. The self-association behavior of TBP in various alkane diluents of different chain lengths (8, 12, and 16 carbons) and a branched alkane (iso-octane) was investigated by Fourier transform infrared spectroscopic measurements. By careful deconvolution of the spectra into multiple peaks, our results indicate that TBP self-associates to form not only dimers, as previous studies showed, but also trimers in the practical concentration range. Using a mathematical fitting procedure, the dimerization and trimerization constants were determined. As expected, these equilibrium constants are dependent on the solvent used. As the alkane chain for linear hydrocarbon solvents becomes longer, dimerization decreases whereas trimerization increases. For the more branched hydrocarbon, we observe a significantly higher dimerization constant. These effects are most likely due to the intermolecular van der Waals interactions between the butyl tails of each TBP molecule and the diluent hydrocarbon chain as all solvents in this study are relatively nonpolar. PMID:27399338

Bacteriorhodopsin (bR) is a unique protein of purple membranes (PMs) of the bacterium Halobacterium salinarum. Tight trimers of this integral photochromic protein form a highly ordered 2D hexagonal crystalline lattice within the PMs. Due to strong excitonic interactions between the bR chromophores (retinals) in the protein trimers, PMs exhibit a strong circular dichroism (CD) activity in the region of the retinal absorption band, which allows monitoring the regularity and stability of the bR trimer organization within the membrane. In this study, the effects of semiconductor quantum dots (QDs) on the bR intramembrane organization and the time course of bR monomerization caused by detergents have been analyzed. The results show that the interaction with QDs does not influence the bR structural organization but considerably accelerates the monomerization of the protein by detergents. These data have been confirmed by the results of atomic force microscopy (AFM) followed by Fourier transform analysis, which have shown that interactions with QDs cause an eightfold acceleration of bR monomerization with Triton. The data show that interactions of nanoparticles with biological membranes may modulate the membrane fluidity and the structural organization and function of integral proteins embedded in these membranes.

By generalizing the traditional single-site strong coupling expansion approach to a cluster one, we study the zero-temperature phase diagram of bosonic atoms in a trimerized Kagomé optical lattice. Some new features are present in this system. Due to the strong intra-trimer hopping interaction, there will be a new Mott insulator (MI), which is by definition incompressible but with a fractional filling per trimer. This is different from the traditional MI, which has an integral filling and originates only from the repulsive interaction between particles. We investigate the MI-to-superfluid transition and the nature of the fractional MI by calculating the critical exponents of phase transitions and the low-lying energy excitation spectra of quasiparticles (quasihole). We will show how the low-energy properties of this system can be understood qualitatively as a Bose–Hubbard model in triangular lattice from the point of view of the cluster strong coupling expansion. We also discuss how our results are related to experiment by studying the Bragg spectroscopy.

Nucleases play important roles in nucleic acid processes, such as replication, repair and recombination. Recently, we identified a novel single-strand specific 3′-5′ exonuclease, PfuExo I, from the hyperthermophilic archaeon Pyrococcus furiosus, which may be involved in the Thermococcales-specific DNA repair system. PfuExo I forms a trimer and cleaves single-stranded DNA at every two nucleotides. Here, we report the structural basis for the cleavage mechanism of this novel exonuclease family. A structural analysis of PhoExo I, the homologous enzyme from P. horikoshii OT3, showed that PhoExo I utilizes an RNase H-like active site and possesses a 3′-OH recognition site ∼9 Å away from the active site, which enables cleavage at every two nucleotides. Analyses of the heterotrimeric and monomeric PhoExo I activities showed that trimerization is indispensable for its processive cleavage mechanism, but only one active site of the trimer is required. PMID:26138487

Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous ligands, is an important extractant used in the solvent extraction process for the recovery of uranium and plutonium from spent nuclear fuel. Microscopic pictures of TBP isomerism and its behavior in n-dodecane diluent were investigated utilizing MD simulations with previously optimized force field parameters for TBP and n-dodecane. Potential mean force (PMF) calculations on a single TBP molecule show seven probable TBP isomers. Radial distribution functions (RDFs) of TBP suggest the existence of TBP trimers at high TBP concentrations in addition to dimers. 2D PMF calculations were performed to determine the angle and distance criteria for TBP trimers. The dimerization and trimerization constants of TBP in n-dodecane were obtained and match our own experimental values using the FTIR technique. The new insights into the conformational behaviors of the TBP molecule as a monomer and as part of an aggregate could greatly aid in the understanding of the complexation between TBP and metal ions in a solvent extraction system. PMID:27398866

By generalizing the traditional single-site strong coupling expansion approach to a cluster one, we study the zero-temperature phase diagram of bosonic atoms in a trimerized Kagomé optical lattice. Some new features are present in this system. Due to the strong intra-trimer hopping interaction, there will be a new Mott insulator (MI), which is by definition incompressible but with a fractional filling per trimer. This is different from the traditional MI, which has an integral filling and originates only from the repulsive interaction between particles. We investigate the MI-to-superfluid transition and the nature of the fractional MI by calculating the critical exponents of phase transitions and the low-lying energy excitation spectra of quasiparticles (quasihole). We will show how the low-energy properties of this system can be understood qualitatively as a Bose-Hubbard model in triangular lattice from the point of view of the cluster strong coupling expansion. We also discuss how our results are related to experiment by studying the Bragg spectroscopy. PMID:27165440

Present paper is the first one in the series devoted to the dynamics of traveling waves emerging in the uncompressed, tri-atomic granular crystals. This work is primarily concerned with the dynamics of one-dimensional periodic granular trimer (tri-atomic) chains in the state of acoustic vacuum. Each unit cell consists of three spherical particles of different masses subject to periodic boundary conditions. Hertzian interaction law governs the mutual interaction of these particles. Under the assumption of zero pre-compression, this interaction is modeled as purely nonlinear, which means the absence of linear force component. The dynamics of such chains is governed by the two system parameters that scale the mass ratios between the particles of the unit cell. Such a system supports two different classes of periodic solutions namely the traveling and standing waves. The primary objective of the present study is the numerical analysis of the bifurcation structure of these solutions with emphasis on the dynamics of traveling waves. In fact, understanding of the bifurcation structure of the traveling wave solutions emerging in the unit-cell granular trimer is rather important and can shed light on the more complex nonlinear wave phenomena emerging in semi-infinite trimer chains.

Peptides derived from the N-terminal heptad repeat (NHR) of HIV-1 gp41 can be potent inhibitors against viral entry when presented in a nonaggregating trimeric coiled-coil conformation via the introduction of exogenous trimerization motifs and intermolecular disulfide bonds. We recently discovered that crosslinking isopeptide bridges within the de novo helical trimers added exceptional resistance to unfolding. Herein, we attempted to optimize (CCIZN17)3, a representative disulfide bond-stabilized chimeric NHR-trimer, by incorporating site-specific interhelical isopeptide bonds as the redox-sensitive disulfide surrogate. In this process, we systematically examined the effect of isopeptide bond position and molecular sizes of auxiliary trimeric coiled-coil motif and NHR fragments on the antiviral potency of these NHR-trimers. Pleasingly, (IZ14N24N)3 possessed promising inhibitory activity against HIV-1 infection and markedly increased proteolytic stability relative to its disulfide-tethered counterpart, suggesting good potential for further development as an effective antiviral agent for treatment of HIV-1 infection. PMID:27562370

Peptides derived from the N-terminal heptad repeat (NHR) of HIV-1 gp41 can be potent inhibitors against viral entry when presented in a nonaggregating trimeric coiled-coil conformation via the introduction of exogenous trimerization motifs and intermolecular disulfide bonds. We recently discovered that crosslinking isopeptide bridges within the de novo helical trimers added exceptional resistance to unfolding. Herein, we attempted to optimize (CCIZN17)3, a representative disulfide bond-stabilized chimeric NHR-trimer, by incorporating site-specific interhelical isopeptide bonds as the redox-sensitive disulfide surrogate. In this process, we systematically examined the effect of isopeptide bond position and molecular sizes of auxiliary trimeric coiled-coil motif and NHR fragments on the antiviral potency of these NHR-trimers. Pleasingly, (IZ14N24N)3 possessed promising inhibitory activity against HIV-1 infection and markedly increased proteolytic stability relative to its disulfide-tethered counterpart, suggesting good potential for further development as an effective antiviral agent for treatment of HIV-1 infection. PMID:27562370

Ab initio calculations at the MP2 level have been performed on water, methanol/water, ethanol/water, and dimethylether/water dimers and on water, methanol/water, and methanol cyclic trimers. Several properties of their hydrogen bonds have been investigated, such as interoxygen distances, O-H bond lengths, binding energies, electronic densities at hydrogen bond (HB) critical points and OH stretch vibrational frequencies. Results exhibit HB enhancements for dimers where the acceptor molecule corresponds to water (HDA dimers) as compared to dimers where the donor is water (HDD dimers). In particular, HB reinforcement depends on the number of alkyl groups bonded to the donor oxygen. For trimers, a comparison among their HB properties and those of dimers shows that HB reinforcements (as compared to isolated dimers) occurring in trimers correlate with HB reinforcements observed in (HDA dimers (as compared to (HDDs). In particular, HB properties of the cyclic water trimer are close to those of alcohol/water HDA dimers, and for the methanol cyclic trimer to that of the dimethylether/water HDA dimer. All of these results agree with an orbital interpretation of hydrogen bonding in terms of charge transfer from donor lone pairs to acceptor antibond σOH*, even if all of the HB properties in cyclic trimers may not be explained from this approach.

Accumulation and deposition of amyloid-β peptide (Aβ) in the brain is a primary cause of the pathogenesis of Alzheimer's disease (AD). Aβ is generated from amyloid-β precursor protein (APP) through sequential cleavages first by β-secretase and then by γ-secretase. Inhibiting β-secretase activity is believed to be one of the most promising strategies for AD treatment. In the present study, we found that a resveratrol trimer, miyabenol C, isolated from stems and leaves of the small-leaf grape (Vitisthunbergii var. taiwaniana), can markedly reduce Aβ and sAPPβ levels in both cell cultures and the brain of AD model mice. Mechanistic studies revealed that miyabenol C affects neither protein levels of APP, the two major α-secretases ADAM10 and TACE, and the γ-secretase component Presenilin 1, nor γ-secretase-mediated Notch processing and TACE activity. In contrast, although miyabenol C has no effect on altering protein levels of the β-secretase BACE1, it can inhibit both in vitro and in vivo β-secretase activity. Together, our results indicate that miyabenol C is a prominent β-secretase inhibitor and lead compound for AD drug development. PMID:25629409

In the catalytic polymerization of 1,3-butadiene during the manufacture of SKD-1 rubber (with titanium and aluminum compounds as catalysts) the toxic oligomers (1,3-butadiene trimers) t,t,t-1, 5,9-cyclododecatriene (I), t,t,c-1, 5,9-cyclododecatriene (II), n-2,4,6,10-dodecatetraene (III), n-1,3,6,10-dodecatertraine (IV), and others end up in the atmosphere and the manufacture of cyclododecane. In the content of the oligomers in the air used for drying the rubber was determined by passing it through active carbon and desorbing the trapped substances with water vapor. However, aspects of the concentration of the microimpurities during their determination in the atmosphere were not considered. The aim of the present work was to develop a gas-chromatographic procedure for the determination of small amounts of compounds in the atmosphere. The tentative safe level amounts to 0.008 mg/m{sup 3} for (I) and 0.01 mg/m{sup 3} for (II, III). In air these oligomers are present in the form of vapor and aerosols. 7 refs., 3 figs., 4 tabs.

Exact quantum dynamics calculations of the eigenstate energy levels and wavefunctions for all bound rovibrational states of the Ne(3) trimer (J = 0-18) have been performed using the ScalIT suite of parallel codes. These codes employ a combination of highly efficient methods, including phase-space optimized discrete variable representation, optimal separable basis, and preconditioned inexact spectral transform methods, together with an effective massive parallelization scheme. The Ne(3) energy levels and wavefunctions were computed using a pair-wise Lennard-Jones potential. Jacobi coordinates were used for the calculations, but to identify just those states belonging to the totally symmetric irreducible representation of the G(12) complete nuclear permutation-inversion group, wavefunctions were plotted in hyperspherical coordinates. "Horseshoe" states were observed above the isomerization barrier, but the horseshoe localization effect is weaker than in Ar(3). The rigid rotor model is found to be applicable for only the ground and first excited vibrational states at low J; fitted rotational constant values are presented. PMID:21913762

Two star-like trimeric cationic surfactants with amide groups in spacers, tri(dodecyldimethylammonioacetoxy)diethyltriamine trichloride (DTAD) and tri(dodecyldimethylammonioacetoxy)tris(2-aminoethyl)amine trichloride (DDAD), have been synthesized, and the aggregation behavior of the surfactants in aqueous solution has been investigated by surface tension, electrical conductivity, isothermal titration microcalorimetry, dynamic light scattering, cryogenic transmission electron microscopy, and NMR techniques. Typically, both the surfactants form vesicles just above critical aggregation concentration (CAC), and then the vesicles transfer to micelles gradually with an increase of the surfactant concentration. It is approved that the conformation of the surfactant molecules changes in this transition process. Just above the CAC, the hydrophobic chains of the surfactant molecules pack more loosely because of the rigid spacer and intramolecular electrostatic repulsion in the three-charged headgroup. With the increase of the surfactant concentration, hydrophobic interaction becomes strong enough to pack the hydrophobic tails tightly and turn the molecular conformation into a pyramid-like shape, thus leading to the vesicle to micelle transition. PMID:20426428

Trimeric intracellular cation-specific (TRIC) channels are integral to muscle excitation–contraction coupling. TRIC channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. Until recently, knowledge of the presence of these proteins was limited to animals. We analyzed the TRIC family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. Prokaryotic members far outnumber eukaryotic members, and although none has been functionally characterized, the evidence suggests that they function as secondary carriers. The presence of fused N- or C-terminal domains of known biochemical functions as well as genomic context analyses provide clues about the functions of these prokaryotic homologs. They are proposed to function in metabolite (e.g., amino acid/ nucleotide) efflux. Phylogenetic analysis revealed that TRIC channel homologs diverged relatively early during evolutionary history and that horizontal gene transfer was frequent in prokaryotes but not in eukaryotes. Topological analyses of TRIC channels revealed that these proteins possess seven putative transmembrane segments (TMSs), which arose by intragenic duplication of a three-TMS polypeptide-encoding genetic element followed by addition of a seventh TMS at the C terminus to give the precursor of all current TRIC family homologs. We propose that this family arose in prokaryotes. PMID:21519847

Biomedical electroactive elastomers with a modulus similar to that of soft tissues are highly desirable for muscle, nerve, and other soft tissue replacement or regeneration, but have rarely been reported. In this work, superiorly stretchable electroactive polyurethane-urea elastomers were designed based on poly(lactide), poly(ethylene glycol), and aniline trimer (AT). A strain at break higher than 1600% and a modulus close to soft tissues was achieved from these copolymers. The mechanisms of super stretchability of the copolymer were systematically investigated. Crystallinity, chemical cross-linking, ionic cross-linking and hard domain formation were examined using differential scanning calorimetry (DSC), X-ray photoelectron spectroscopy (XPS), dynamic light scattering (DLS), nuclear magnetic resonance (NMR) measurements and transmission electron microscopy (TEM). The sphere-like hard domains self-assembled from AT segments were found to provide the crucial physical interactions needed for the novel super elastic material formation. These super stretchable copolymers were blended with conductive fillers such as polyaniline nanofibers and nanosized carbon black to achieve a high electric conductivity of 0.1 S/cm while maintaining an excellent stretchability and a modulus similar to that of soft tissues (lower than 10 MPa). PMID:26692638

We consider time-periodic structures of granular crystals consisting of alternate chrome steel (S) and tungsten carbide (W) spherical particles where each unit cell follows the pattern of a 2 : 1 trimer: S-W-S. The configuration at the left boundary is driven by a harmonic in-time actuation with given amplitude and frequency while the right one is a fixed wall. Similar to the case of a dimer chain, the combination of dissipation, driving of the boundary, and intrinsic nonlinearity leads to complex dynamics. For fixed driving frequencies in each of the spectral gaps, we find that the nonlinear surface modes and the statesmore » dictated by the linear drive collide in a saddle-node bifurcation as the driving amplitude is increased, beyond which the dynamics of the system becomes chaotic. While the bifurcation structure is similar for solutions within the first and second gap, those in the first gap appear to be less robust. We also conduct a continuation in driving frequency, where it is apparent that the nonlinearity of the system results in a complex bifurcation diagram, involving an intricate set of loops of branches, especially within the spectral gap. The theoretical findings are qualitatively corroborated by the experimental full-field visualization of the time-periodic structures.« less

ABSTRACT Glycosylation is a widespread mechanism employed by both eukaryotes and bacteria to increase the functional diversity of their proteomes. The nontypeable Haemophilus influenzae glycosyltransferase HMW1C mediates unconventional N-linked glycosylation of the adhesive protein HMW1, which is encoded in a two-partner secretion system gene cluster that also encodes HMW1C. In this system, HMW1 is modified in the cytoplasm by sequential transfer of hexose residues. In the present study, we examined Kingella kingae and Aggregatibacter aphrophilus homologues of HMW1C that are not encoded near a gene encoding an obvious acceptor protein. We found both homologues to be functional glycosyltransferases and identified their substrates as the K. kingae Knh and the A. aphrophilus EmaA trimeric autotransporter proteins. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed multiple sites of N-linked glycosylation on Knh and EmaA. Without glycosylation, Knh and EmaA failed to facilitate wild-type levels of bacterial autoaggregation or adherence to human epithelial cells, establishing that glycosylation is essential for proper protein function. PMID:26307167

Signal transduction via integrins and G protein–coupled receptors is critical to control cell behavior. These two receptor classes have been traditionally believed to trigger distinct and independent signaling cascades in response to extracellular cues. Here, we report a novel mechanism of integrin signaling that requires activation of the trimeric G protein Gαi by the nonreceptor guanine nucleotide exchange factor (GEF) GIV (also known as Girdin), a metastasis-associated protein. We demonstrate that GIV enhances integrin-dependent cell responses upon extracellular matrix stimulation and makes tumor cells more invasive. These responses include remodeling of the actin cytoskeleton and PI3K-dependent signaling, resulting in enhanced haptotaxis and invasion. We show that both GIV and its substrate Gαi3 are recruited to active integrin complexes and that tumor cells engineered to express GEF-deficient GIV fail to transduce integrin signals into proinvasive responses via a Gβγ-PI3K axis. Our discoveries delineate a novel mechanism by which integrin signaling is rewired during metastasis to result in increased tumor invasiveness. PMID:26391662

Multi-particle potential surfaces have a number of characteristics that are absent from the more familiar two-body potentials of their constituents. Specifically in the case of triatomic alkali systems, the lowest two doublet surfaces are degenerate at specific locations commonly known as conical intersections. The collection of these points of intersection form a ``seam'' that trace out a line in nuclear space. As the complex propagates along the reaction path, the degeneracy at the seam allows for a radiationless transition between the surfaces. Here we analyze the lower two doublet states of the KRbK trimer. First, we map out the seam of intersections throughout the nuclear space and determine branching vectors that provide an accurate description of spatial derivative couplings in the vicinity of conical intersections and characterize the subsequent dynamics in the immediate region. We also revisit classical simulations of the nuclear motion on multiple surfaces and investigate how chaotic motion on the complex surfaces affect the reaction in the ultracold domain. This work is supported by the ARO-MURI and NSF grants.

Proanthocyanidins are abundant in peanut skin, and in this study, the antibacterial effects of a peanut skin extract (PSE) against food-borne bacteria were investigated to find its minimum inhibitory concentration. Food-borne gram-positive bacteria, and in particular Bacillus cereus, was more sensitive to PSE. In particular, the inhibitory activity of epicatechin-(4β → 6)-epicatechin-(2β → O→7, 4β → 8)-catechin (EEC), a proanthocyanidin trimer from peanut skin, against B. cereus was stronger than that of procyanidin A1, a proanthocyanidin dimer. DNA microarray analysis of B. cereus treated with EEC was carried out, with a finding that 597 genes were significantly up-regulated. Analysis of the up-regulated genes suggested that EEC disrupted the normal condition of the cell membrane and wall of B. cereus and alter its usual nutritional metabolism. Moreover, treatment of B. cereus with EEC inhibited glucose uptake, suggesting that EEC affects the cell-surface adsorption. PMID:27061585

Gephyrin is a ubiquitously expressed protein that, in the central nervous system, forms a submembraneous scaffold for anchoring inhibitory neurotransmitter receptors in the postsynaptic membrane. The N- and C-terminal domains of gephyrin are homologous to the Escherichia coli enzymes MogA and MoeA, respectively, both of which are involved in molybdenum cofactor biosynthesis. This enzymatic pathway is highly conserved from bacteria to mammals, as underlined by the ability of gephyrin to rescue molybdenum cofactor deficiencies in different organisms. Here we report the x-ray crystal structure of the N-terminal domain (amino acids 2-188) of rat gephyrin at 1.9-A resolution. Gephyrin-(2-188) forms trimers in solution, and a sequence motif thought to be involved in molybdopterin binding is highly conserved between gephyrin and the E. coli protein. The atomic structure of gephyrin-(2-188) resembles MogA, albeit with two major differences. The path of the C-terminal ends of gephyrin-(2-188) indicates that the central and C-terminal domains, absent in this structure, should follow a similar 3-fold arrangement as the N-terminal region. In addition, a central beta-hairpin loop found in MogA is lacking in gephyrin-(2-188). Despite these differences, both structures show a high degree of surface charge conservation, which is consistent with their common catalytic function. PMID:11325967

The C-terminal soluble domain of stomatin operon partner protein (STOPP) of the hyperthermophilic archaeon Pyrococcus horikoshii has an oligonucleotide binding-fold (OB-fold). STOPP lacks the conserved surface residues necessary for binding to DNA/RNA. A tryptophan (W) residue is conserved instead at the molecular surface. Solvent-accessible W residues are often found at interfaces of protein-protein complexes, which suggested the possibility of self-assembling of STOPP. Protein-protein interactions among the C-terminal soluble domains of STOPP PH1510 (1510-C) were then analyzed by chemical linking and blue native polyacrylamide gel electrophoresis (BN-PAGE) methods. These results suggest that the soluble domains of STOPP could assemble into homo-oligomers. Since hexameric subcomplex I from archaeal proteasome consists of coiled-coil segments and OB-fold domains, molecular modeling of 1510-C was performed using hexameric subcomplex I as a template. Although 1510-C is a comparatively small polypeptide consisting of approximately 60 residues, numerous salt bridges and hydrophobic interactions were observed in the predicted hexamer of 1510-C, suggesting the stability of the homo-oligomeric structure. This oligomeric property of STOPP may be favorable for triplicate proteolysis of the trimer of prokaryotic stomatin. PMID:23587725

Accumulation and deposition of amyloid-β peptide (Aβ) in the brain is a primary cause of the pathogenesis of Alzheimer’s disease (AD). Aβ is generated from amyloid-β precursor protein (APP) through sequential cleavages first by β-secretase and then by γ-secretase. Inhibiting β-secretase activity is believed to be one of the most promising strategies for AD treatment. In the present study, we found that a resveratrol trimer, miyabenol C, isolated from stems and leaves of the small-leaf grape (Vitisthunbergii var. taiwaniana), can markedly reduce Aβ and sAPPβ levels in both cell cultures and the brain of AD model mice. Mechanistic studies revealed that miyabenol C affects neither protein levels of APP, the two major α-secretases ADAM10 and TACE, and the γ-secretase component Presenilin 1, nor γ-secretase-mediated Notch processing and TACE activity. In contrast, although miyabenol C has no effect on altering protein levels of the β-secretase BACE1, it can inhibit both in vitro and in vivo β-secretase activity. Together, our results indicate that miyabenol C is a prominent β-secretase inhibitor and lead compound for AD drug development. PMID:25629409

A halogen atom/metal vapor laser is discussed in terms of CW power and performance. Fluorine and sodium represent surrogates for the halogen and metal species; other combinations are possible. Since lasing may occur from a variety of excited electronic states, operation is expected to be broadly dispersed over the visible and near UV wavelength regions. The device is a low pressure, supersonic mixing laser that resembles the HF/DF CW laser, e.g., separate plenums are utilized for the fluorine and sodium vapors, and each plenum feeds a nozzle array. Sodium trimer formation begins in the nozzle and continues inside the laser cavity. The design of this nozzle is particularly important; the concept of controlled condensation is introduced. Downstream of the nozzle bank, the two vapor streams mix and the F-Na3 reaction pumps several electronically excited states that have gain in the blue-green region. Estimates are given for power per unit mass flow rate and power per unit nozzle bank cross-sectional area.

We have previously observed that while native Treponema pallidum rare outer membrane protein 1 (Tromp1) is hydrophobic and has porin activity, recombinant forms of Tromp1 do not possess these properties. In this study we show that these properties are determined by conformation and can be replicated by proper renaturation of recombinant Tromp1. Native Tromp1, but not the 47-kDa lipoprotein, extracted from whole organisms by using Triton X-114, was found to lose hydrophobicity after treatment in 8 M urea, indicating that Tromp1’s hydrophobicity is conformation dependent. Native Tromp1 was purified from 0.1% Triton X-100 extracts of whole organisms by fast-performance liquid chromatography (FPLC) and shown to have porin activity in planar lipid bilayers. Cross-linking studies of purified native Tromp1 with an 11 Å cross-linking agent showed oligomeric forms consistent with dimers and trimers. For renaturation studies of recombinant Tromp1 (rTromp1), a 31,109-Da signal-less construct was expressed in Escherichia coli and purified by FPLC. FPLC-purified rTromp1 was denatured in 8 M urea and then renatured in the presence of 0.5% Zwittergent 3,14 during dialysis to remove the urea. Renatured rTromp1 was passed through a Sephacryl S-300 gel exclusion column previously calibrated with known molecular weight standards. While all nonrenatured rTromp1 eluted from the column at approximately the position of the carbonic anhydrase protein standard (29 kDa), all renatured rTromp1 eluted at the position of the phosphorylase b protein standard (97 kDa), suggesting a trimeric conformation. Trimerization was confirmed by using an 11 Å cross-linking agent which showed both dimers and trimers similar to that of native Tromp1. Triton X-114 phase separations showed that all of renatured rTromp1, but none of nonrenatured rTromp1, phase separated exclusively into the hydrophobic detergent phase, similar to native Tromp1. Circular dichroism of nonrenatured and renatured rTromp1

The autotransporters are a large and diverse family of bacterial secreted and outer membrane proteins, which are present in many Gram-negative bacterial pathogens and play a role in numerous environmental and virulence-associated interactions. As part of a larger systematic study on the autotransporters of Burkholderia pseudomallei, the causative agent of the severe tropical disease melioidosis, we have constructed an insertion mutant in the bpss1439 gene encoding an unstudied predicted trimeric autotransporter adhesin. The bpss1439 mutant demonstrated a significant reduction in biofilm formation at 48 hours in comparison to its parent 10276 wild-type strain. This phenotype was complemented to wild-type levels by the introduction of a full-length copy of the bpss1439 gene in trans. Examination of the wild-type and bpss1439 mutant strains under biofilm-inducing conditions by microscopy after 48 hours confirmed that the bpss1439 mutant produced less biofilm compared to wild-type. Additionally, it was observed that this phenotype was due to low levels of bacterial adhesion to the abiotic surface as well as reduced microcolony formation. In a murine melioidosis model, the bpss1439 mutant strain demonstrated a moderate attenuation for virulence compared to the wild-type strain. This attenuation was abrogated by in trans complementation, suggesting that bpss1439 plays a subtle role in the pathogenesis of B. pseudomallei. Taken together, these studies indicate that BPSS1439 is a novel predicted autotransporter involved in biofilm formation of B. pseudomallei; hence, this factor was named BbfA, Burkholderia biofilm factor A. PMID:24223950

Pbx/exd proteins modulate the DNA binding affinities and specificities of Hox proteins and contribute to the execution of Hox-dependent developmental programs in arthropods and vertebrates. Pbx proteins also stably heterodimerize and bind DNA with Meis and Pknox1-Prep1, additional members of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins that function on common genetic pathways with a subset of Hox proteins. In this study, we demonstrated that Pbx and Meis bind DNA as heterotrimeric complexes with Hoxb1 on a genetically defined Hoxb2 enhancer, r4, that mediates the cross-regulatory transcriptional effects of Hoxb1 in vivo. The DNA binding specificity of the heterotrimeric complex for r4 is mediated by a Pbx-Hox site in conjunction with a distal Meis site, which we showed to be required for ternary complex formation and Meis-enhanced transcription. Formation of heterotrimeric complexes in which all three homeodomains bind their cognate DNA sites is topologically facilitated by the ability of Pbx and Meis to interact through their amino termini and bind DNA without stringent half-site orientation and spacing requirements. Furthermore, Meis site mutation in the Hoxb2 enhancer phenocopies Pbx-Hox site mutation to abrogate enhancer-directed expression of a reporter transgene in the murine embryonic hindbrain, demonstrating that DNA binding by all three proteins is required for trimer function in vivo. Our data provide in vitro and in vivo evidence for the combinatorial regulation of Hox and TALE protein functions that are mediated, in part, by their interdependent DNA binding activities as ternary complexes. As a consequence, Hoxb1 employs Pbx and Meis-related proteins, as a pair of essential cofactors in a higher-order molecular complex, to mediate its transcriptional effects on an endogenous Hox response element. PMID:10373562

Bacterial biofilms resist host defenses and antibiotics partly because of their decreased metabolism. Some bacteria use proinflammatory cytokines, such as interleukin (IL)-1β, as cues to promote biofilm formation and to alter virulence. Although one potential bacterial IL-1β receptor has been identified, current knowledge of the bacterial IL-1β sensing mechanism is limited. In chronic biofilm infection, periodontitis, Aggregatibacter actinomycetemcomitans requires tight adherence (tad)-locus to form biofilms, and tissue destroying active lesions contain more IL-1β than inactive ones. The effect of IL-1β on the metabolic activity of A. actinomycetemcomitans biofilm was tested using alamarBlue™. The binding of IL-1β to A. actinomycetemcomitans cells was investigated using transmission electron microscopy and flow cytometry. To identify the proteins which interacted with IL-1β, different protein fractions from A. actinomycetemcomitans were run in native-PAGE and blotted using biotinylated IL-1β and avidin-HRP, and identified using mass spectroscopy. We show that although IL-1β slightly increases the biofilm formation of A. actinomycetemcomitans, it reduces the metabolic activity of the biofilm. A similar reduction was observed with all tad-locus mutants except the secretin mutant, although all tested mutant strains as well as wild type strains bound IL-1β. Our results suggest that IL-1β might be transported into the A. actinomycetemcomitans cells, and the trimeric form of intracellular ATP synthase subunit β interacted with IL-1β, possibly explaining the decreased metabolic activity. Because ATP synthase is highly conserved, it might universally enhance biofilm resistance to host defense by binding IL-1β during inflammation. PMID:21533109

Despite almost 30 years of research, no effective vaccine has yet been developed against HIV-1. Probably such a vaccine would need to induce both an effective T cell and antibody response. Any vaccine component focused on inducing humoral immunity requires the HIV-1 envelope (Env) glycoprotein complex as it is the only viral protein exposed on the virion surface. HIV-1 has evolved several mechanisms to evade broadly reactive neutralizing antibodies. One such a mechanism involves variable loop domains, which are highly flexible structures that shield the underlying conserved epitopes. We hypothesized that removal of such loops would increase the exposure and immunogenicity of these conserved regions. Env variable loop deletion however often leads to protein misfolding and aggregation because hydrophobic patches becoming solvent accessible. We have therefore previously used virus evolution to acquire functional Env proteins lacking the V1V2 loop. We then expressed them in soluble (uncleaved) gp140 forms. Three mutants were found to perform optimally in terms of protein expression, stability, trimerization and folding. In this study, we characterized the immune responses to these antigens in rabbits. The V1V2 deletion mutant ΔV1V2.9.VK induced a prominent response directed to epitopes that are not fully available on the other Env proteins tested but that effectively bound and neutralized the ΔV1V2 Env virus. This Env variant also induced more efficient neutralization of the tier 1 virus SF162. The immune refocusing effect was lost after booster immunization with a full-length gp140 protein with intact V1V2 loops. Collectively, this result suggests that deletion of variable domains could alter the specificity of the humoral immune response, but did not result in broad neutralization of neutralization-resistant virus isolates. PMID:23840716

Trimeric G protein signaling is a fundamental mechanism of cellular communication in eukaryotes. The core of this mechanism consists of activation of G proteins by the guanine-nucleotide exchange factor (GEF) activity of G protein coupled receptors. However, the duration and amplitude of G protein-mediated signaling are controlled by a complex network of accessory proteins that appeared and diversified during evolution. Among them, nonreceptor proteins with GEF activity are the least characterized. We recently found that proteins of the ccdc88 family possess a Gα-binding and activating (GBA) motif that confers GEF activity and regulates mammalian cell behavior. A sequence similarity-based search revealed that ccdc88 genes are highly conserved across metazoa but the GBA motif is absent in most invertebrates. This prompted us to investigate whether the GBA motif is present in other nonreceptor proteins in invertebrates. An unbiased bioinformatics search in Caenorhabditis elegans identified GBAS-1 (GBA and SPK domain containing-1) as a GBA motif-containing protein with homologs only in closely related worm species. We demonstrate that GBAS-1 has GEF activity for the nematode G protein GOA-1 and that the two proteins are coexpressed in many cells of living worms. Furthermore, we show that GBAS-1 can activate mammalian Gα-subunits and provide structural insights into the evolutionarily conserved determinants of the GBA–G protein interface. These results demonstrate that the GBA motif is a functional GEF module conserved among highly divergent proteins across evolution, indicating that the GBA-Gα binding mode is strongly constrained under selective pressure to mediate receptor-independent G protein activation in metazoans. PMID:26659249

Pbx/exd proteins modulate the DNA binding affinities and specificities of Hox proteins and contribute to the execution of Hox-dependent developmental programs in arthropods and vertebrates. Pbx proteins also stably heterodimerize and bind DNA with Meis and Pknox1-Prep1, additional members of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins that function on common genetic pathways with a subset of Hox proteins. In this study, we demonstrated that Pbx and Meis bind DNA as heterotrimeric complexes with Hoxb1 on a genetically defined Hoxb2 enhancer, r4, that mediates the cross-regulatory transcriptional effects of Hoxb1 in vivo. The DNA binding specificity of the heterotrimeric complex for r4 is mediated by a Pbx-Hox site in conjunction with a distal Meis site, which we showed to be required for ternary complex formation and Meis-enhanced transcription. Formation of heterotrimeric complexes in which all three homeodomains bind their cognate DNA sites is topologically facilitated by the ability of Pbx and Meis to interact through their amino termini and bind DNA without stringent half-site orientation and spacing requirements. Furthermore, Meis site mutation in the Hoxb2 enhancer phenocopies Pbx-Hox site mutation to abrogate enhancer-directed expression of a reporter transgene in the murine embryonic hindbrain, demonstrating that DNA binding by all three proteins is required for trimer function in vivo. Our data provide in vitro and in vivo evidence for the combinatorial regulation of Hox and TALE protein functions that are mediated, in part, by their interdependent DNA binding activities as ternary complexes. As a consequence, Hoxb1 employs Pbx and Meis-related proteins, as a pair of essential cofactors in a higher-order molecular complex, to mediate its transcriptional effects on an endogenous Hox response element. PMID:10373562

Tobacco addiction represents one of the largest public health problems in the world and is the leading cause of cancer and heart disease, resulting in millions of deaths a year. Vaccines for smoking cessation have shown considerable promise in preclinical models, although functional antibody responses induced in humans are only modestly effective in preventing nicotine entry into the brain. The challenge in generating serum antibodies with a large nicotine binding capacity is made difficult by the fact that this drug is non-immunogenic and must be conjugated as a hapten to a protein carrier. To circumvent the limitations of traditional carriers like keyhole limpet hemocyanin (KLH), we have synthesized a short trimeric coiled-coil peptide (TCC) that creates a series of B and T cell epitopes with uniform stoichiometry and high density. Here we compared the relative activities of a TCC-nic vaccine and two control KLH-nic vaccines using Alum as an adjuvant or GLA-SE, which contains a synthetic TLR4 agonist formulated in a stable oil-in-water emulsion. The results showed that the TCC's high hapten density correlated with a better immune response in mice as measured by anti-nicotine Ab titer, affinity, and specificity, and was responsible for a reduction in anti-carrier immunogenicity. The Ab responses achieved with this synthetic vaccine resulted in a nicotine binding capacity in serum that could prevent >90% of a nicotine dose equivalent to three smoked cigarettes (0.05 mg/kg) from reaching the brain. PMID:25494044

Trimeric G protein signaling is a fundamental mechanism of cellular communication in eukaryotes. The core of this mechanism consists of activation of G proteins by the guanine-nucleotide exchange factor (GEF) activity of G protein coupled receptors. However, the duration and amplitude of G protein-mediated signaling are controlled by a complex network of accessory proteins that appeared and diversified during evolution. Among them, nonreceptor proteins with GEF activity are the least characterized. We recently found that proteins of the ccdc88 family possess a Gα-binding and activating (GBA) motif that confers GEF activity and regulates mammalian cell behavior. A sequence similarity-based search revealed that ccdc88 genes are highly conserved across metazoa but the GBA motif is absent in most invertebrates. This prompted us to investigate whether the GBA motif is present in other nonreceptor proteins in invertebrates. An unbiased bioinformatics search in Caenorhabditis elegans identified GBAS-1 (GBA and SPK domain containing-1) as a GBA motif-containing protein with homologs only in closely related worm species. We demonstrate that GBAS-1 has GEF activity for the nematode G protein GOA-1 and that the two proteins are coexpressed in many cells of living worms. Furthermore, we show that GBAS-1 can activate mammalian Gα-subunits and provide structural insights into the evolutionarily conserved determinants of the GBA-G protein interface. These results demonstrate that the GBA motif is a functional GEF module conserved among highly divergent proteins across evolution, indicating that the GBA-Gα binding mode is strongly constrained under selective pressure to mediate receptor-independent G protein activation in metazoans. PMID:26659249

Eukaryotes rely on efficient distribution of energy and carbon skeletons between organs in the form of sugars. Glucose in animals and sucrose in plants serve as dominant distribution forms. Cellular sugar uptake and release require vesicular and/or plasma membrane transport proteins. Humans and plants use related proteins from three superfamilies for sugar translocation: the major facilitator superfamily (MFS), the sodium solute symporter Family (SSF; only animal kingdom), and SWEETs1-5. SWEETs carry mono- and disaccharides6 across vacuolar or plasma membranes. Plant SWEETs play key roles in sugar translocation between compartments, cells, and organs, notably in nectar secretion7, phloem loading for long distance translocation8, pollen nutrition9, and seed filling10. Plant SWEETs cause pathogen susceptibility by sugar leakage from infected cells3,11,12. The vacuolar AtSWEET2 sequesters sugars in root vacuoles; loss-of-function increases susceptibility to Pythium infection13. Here we show that its orthologue, the vacuolar glucose transporter OsSWEET2b from rice, consists of an asymmetrical pair of triple-helix-bundles (THBs), connected by an inversion linker helix (TM4) to create the translocation pathway. Structural and biochemical analyses show OsSWEET2b in an apparent inward (cytosolic) open state forming homomeric trimers. TM4 tightly interacts with the first THB within a protomer and mediates key contacts among protomers. Structure-guided mutagenesis of the close paralogue SWEET1 from Arabidopsis identified key residues in substrate translocation and protomer crosstalk. Insights into the structure-function relationship of SWEETs is valuable for understanding the transport mechanism of eukaryotic SWEETs and may be useful for engineering sugar flux. PMID:26479032

Interactions of trianionic curcumin (Cur(3-)) with a series of cationic surfactants, monomeric surfactant dodecyl trimethylammonium bromide (DTAB), dimeric surfactant hexamethylene-1,6-bis(dodecyldimethylammonium bromide) (12-6-12) and trimeric surfactant tri(dodecyldimethylammonioacetoxy)diethyltriamine trichloride (DTAD), have been investigated in aqueous solution of pH 13.0. Surface tension and spectral measurements indicate that the cationic surfactants display a similar surfactant concentration dependent interaction process with Cur(3-), involving three interaction stages. At first the three cationic surfactants electrostatically bind on Cur(3-) to form the surfactant-Cur(3-) complex. Then the bound and unbound cationic surfactants with Cur(3-) aggregate into surfactant-Cur(3-) mixed micelles through hydrophobic interactions above the critical micelle concentration of the surfactants (CMCC) in the presence of Cur(3-). Finally excess unbound surfactants self-assemble into micelles like those without Cur(3-). For all the three surfactants, the addition of Cur(3-) only decreases the critical micelle concentration of 12-6-12 but does not affect the critical micelle concentration of DTAB and DTAD. As the oligomeric degree of surfactants increases, the intermolecular interaction of the cationic surfactants with Cur(3-) increases and the surfactant amount needed for Cur(3-) encapsulation decreases. Compared with 12-6-12, either the weaker interaction of DTAB with Cur(3-) or stronger interaction of DTAD with Cur(3-) limits the stability or solubility of Cur(3-) in surfactant micelles. Therefore, gemini surfactant 12-6-12 is the best choice to effectively suppress Cur(3-) degradation at very low concentrations. Isothermal titration microcalorimetry, surface tension and (1)H NMR results reveal that 12-6-12 and Cur(3-) form a (12-6-12)2-Cur(3-) complex and start to form micelles at extremely decreased concentrations, where either 12-6-12 or Cur(3-) works as a bridge

Haemophilus ducreyi is the causative agent of the sexually transmitted genital ulcer disease chancroid. Strains of H. ducreyi are grouped in two classes (I and II) based on genotypic and phenotypic differences, including those found in DsrA, an outer membrane protein belonging to the family of multifunctional trimeric autotransporter adhesins. DsrA is a key serum resistance factor of H. ducreyi that prevents binding of natural IgM at the bacterial surface and functions as an adhesin to fibronectin, fibrinogen, vitronectin, and human keratinocytes. Monoclonal antibodies (MAbs) were developed to recombinant DsrA (DsrAI) from prototypical class I strain 35000HP to define targets for vaccine and/or therapeutics. Two anti-DsrAI MAbs bound monomers and multimers of DsrA from genital and non-genital/cutaneous H. ducreyi strains in a Western blot and reacted to the surface of the genital strains; however, these MAbs did not recognize denatured or native DsrA from class II strains. In a modified extracellular matrix protein binding assay using viable H. ducreyi, one of the MAbs partially inhibited binding of fibronectin, fibrinogen, and vitronectin to class I H. ducreyi strain 35000HP, suggesting a role for anti-DsrA antibodies in preventing binding of H. ducreyi to extracellular matrix proteins. Standard ELISA and surface plasmon resonance using a peptide library representing full-length, mature DsrAI revealed the smallest nominal epitope bound by one of the MAbs to be MEQNTHNINKLS. Taken together, our findings suggest that this epitope is a potential target for an H. ducreyi vaccine. PMID:25897604

The transitioning of the ectodomain of gp41 from a pre-hairpin to a six-helix bundle conformation is a crucial aspect of virus-cell fusion. To gain insight into the intermediary steps of the fusion process we have studied the pH and dodecyl phosphocholine (DPC) micelle dependent trimer association of gp41 by systematic deletion analysis of an optimized construct termed 17–172 (residues 528 to 683 of Env) that spans the fusion peptide proximal region (FPPR) to the membrane proximal external region (MPER) of gp41, by sedimentation velocity and double electron-electron resonance (DEER) EPR spectroscopy. Trimerization at pH 7 requires the presence of both the FPPR and MPER regions. However, at pH 4, the protein completely dissociates to monomers. DEER measurements reveal a partial fraying of the C-terminal MPER residues in the 17–172 trimer while the other regions, including the FPPR, remain compact. In accordance, truncating nine C-terminal MPER residues (675–683) in the 17–172 construct does not shift the trimer-monomer equilibrium significantly. Thus, in the context of the gp41 ectodomain spanning residues 17–172, trimerization is clearly dependent on FPPR and MPER regions even when the terminal residues of MPER unravel. The antibody Z13e1, which spans both the 2F5 and 4E10 epitopes in MPER, binds to 17–172 with a Kd of 1 ± 0.12 μM. Accordingly, individual antibodies 2F5 and 4E10 also recognize the 17–172 trimer/DPC complex. We propose that binding of the C-terminal residues of MPER to the surface of the DPC micelles models a correct positioning of the trimeric transmembrane domain anchored in the viral membrane. PMID:27513582

The transitioning of the ectodomain of gp41 from a pre-hairpin to a six-helix bundle conformation is a crucial aspect of virus-cell fusion. To gain insight into the intermediary steps of the fusion process we have studied the pH and dodecyl phosphocholine (DPC) micelle dependent trimer association of gp41 by systematic deletion analysis of an optimized construct termed 17-172 (residues 528 to 683 of Env) that spans the fusion peptide proximal region (FPPR) to the membrane proximal external region (MPER) of gp41, by sedimentation velocity and double electron-electron resonance (DEER) EPR spectroscopy. Trimerization at pH 7 requires the presence of both the FPPR and MPER regions. However, at pH 4, the protein completely dissociates to monomers. DEER measurements reveal a partial fraying of the C-terminal MPER residues in the 17-172 trimer while the other regions, including the FPPR, remain compact. In accordance, truncating nine C-terminal MPER residues (675-683) in the 17-172 construct does not shift the trimer-monomer equilibrium significantly. Thus, in the context of the gp41 ectodomain spanning residues 17-172, trimerization is clearly dependent on FPPR and MPER regions even when the terminal residues of MPER unravel. The antibody Z13e1, which spans both the 2F5 and 4E10 epitopes in MPER, binds to 17-172 with a Kd of 1 ± 0.12 μM. Accordingly, individual antibodies 2F5 and 4E10 also recognize the 17-172 trimer/DPC complex. We propose that binding of the C-terminal residues of MPER to the surface of the DPC micelles models a correct positioning of the trimeric transmembrane domain anchored in the viral membrane. PMID:27513582

The human immunodeficiency virus type 1 (HIV-1) surface envelope glycoprotein (Env) complex, a homotrimer containing gp120 surface glycoprotein and gp41 transmembrane glycoprotein subunits, mediates the binding and fusion of the virus with susceptible target cells. The Env complex is the target for neutralizing antibodies (NAbs) and is the basis for vaccines intended to induce NAbs. Early generation vaccines based on monomeric gp120 subunits did not confer protection from infection; one alternative approach is therefore to make and evaluate soluble forms of the trimeric Env complex. We have directly compared the immunogenicity in rabbits of two forms of soluble trimeric Env and monomeric gp120 based on the sequence of HIV-1{sub JR-FL}. Both protein-only and DNA-prime, protein-boost immunization formats were evaluated, DNA-priming having little or no influence on the outcome. One form of trimeric Env was made by disrupting the gp120-gp41 cleavage site by mutagenesis (gp140{sub UNC}), the other contains an intramolecular disulfide bond to stabilize the cleaved gp120 and gp41 moieties (SOSIP.R6 gp140). Among the three immunogens, SOSIP.R6 gp140 most frequently elicited neutralizing antibodies against the homologous, neutralization-resistant strain, HIV-1{sub JR-FL}. All three proteins induced NAbs against more sensitive strains, but the breadth of activity against heterologous primary isolates was limited. When antibodies able to neutralize HIV-1{sub JR-FL} were detected, antigen depletion studies showed they were not directed at the V3 region but were targeted at other, undefined gp120 and also non-gp120 epitopes.

The human islet amyloid polypeptide (hIAPP) or amylin is a 37-residue hormone found as amyloid deposits in pancreatic extracts of nearly all type 2 diabetes patients. The fragment 20-29 of sequence SNNFGAILSS (hIAPP20-29) has been shown to be responsible for the amyloidogenic propensities of the full length protein. Various polymorphic forms of hIAPP20-29 fibrils were described by using Fourier transform infrared (FTIR) and solid-state NMR experiments: unseeded hIAPP20-29 fibril with out-of-register antiparallel β-strands, and two forms of seeded hIAPP20-29 fibril, with in-register antiparallel or in-register parallel β-strands. As a first step toward understanding this polymorphism, we explore the equilibrium structures of the soluble hIAPP20-29 trimer, using multiple molecular dynamics (MD) simulations with the Optimized Potential for Efficient structure Prediction (OPEP) coarse-grained implicit solvent force field for a total length of 3.2 μs. Although, the trimer is found mainly random coil, consistent with the signal measured experimentally during the lag phase of hIAPP20-29 fibril formation, the central FGAIL residues have a relative high propensity to form interpeptide β-sheets and antiparallel β-strands are more probable than parallel β-strands. One MD-predicted out-of-register antiparallel three-stranded β-sheet matches exactly the FTIR-derived unseeded hIAPP20-29 fibril model. Our simulations, however, do not reveal any evidence of in-register parallel or in-register antiparallel β-sheets as reported for seeded hIAPP20-29 fibrils. All these results indicate that fibril polymorphism is partially encoded in a trimer.

Surfactant protein A2 (SP-A2) plays an essential role in surfactant metabolism and lung host defense. SP-A2 mutations in the carbohydrate recognition domain have been related to familial pulmonary fibrosis and can lead to a recombinant protein secretion deficiency in vitro. In this study, we explored the molecular mechanism of protein secretion deficiency and the subsequent biological effects in CHO-K1 cells expressing both wild-type and several different mutant forms of SP-A2. We demonstrate that the SP-A2 G231V and F198S mutants impair the formation of dimmer/trimer SP-A2 which contributes to the protein secretion defect. A deficiency in sialylation, but not N-linked glycosylation, is critical to the observed dimmer/trimer impairment-induced secretion defect. Furthermore, both mutant forms accumulate in the ER and form NP-40-insoluble aggregates. In addition, the soluble mutant SP-A2 could be partially degraded through the proteasome pathway but not the lysosome or autophagy pathway. Intriguingly, 4-phenylbutyrate acid (4-PBA), a chemical chaperone, alleviates aggregate formation and partially rescued the protein secretion of SP-A2 mutants. In conclusion, SP-A2 G231V and F198S mutants impair the dimmer/trimer assembly, which contributes to the protein sialylation and secretion deficiency. The intracellular protein mutants could be partially degraded through the proteasome pathway and also formed aggregates. The treatment of the cells with 4-PBA resulted in reduced aggregation and rescued the secretion of mutant SP-A2. PMID:23056344

Licanantase (Lic) is the major component of the secretome of Acidithiobacillus thiooxidans when grown in elemental sulphur. When used as an additive, Lic improves copper recovery from bioleaching processes. However, this recovery enhancement is not fully understood. In this context, our aim is to predict the 3D structure of Lic, to shed light on its structure-function relationships. Bioinformatics analyses on the amino acid sequence of Lic showed a great similarity with Lpp, an Escherichia coli Lipoprotein that can form stable trimers in solution. Lic and Lpp share the secretion motif, intracellular processing and alpha helix structure, as well as the distribution of hydrophobic residues in heptads forming a hydrophobic core, typical of coiled-coil structures. Cross-linking experiments showed the presence of Lic trimers, supporting our predictions. Taking the in vitro and in silico evidence as a whole, we propose that the most probable structure for Lic is a trimeric coiled-coil. According to this prediction, a suitable model for Lic was produced using the de novo algorithm “Rosetta Fold-and-Dock”. To assess the structural stability of our model, Molecular Dynamics (MD) and Replica Exchange MD simulations were performed using the structure of Lpp and a 14-alanine Lpp mutant as controls, at both acidic and neutral pH. Our results suggest that Lic was the most stable structure among the studied proteins in both pH conditions. This increased stability can be explained by a higher number of both intermonomer hydrophobic contacts and hydrogen bonds, key elements for the stability of Lic’s secondary and tertiary structure. PMID:25165619

Monomeric HIV envelope vaccines fail to elicit broadly neutralizing antibodies or to protect against infection. Neutralizing antibodies against HIV bind to native, functionally active Env trimers on the virion surface. Gag-Env pseudovirions recapitulate the native trimer, and could serve as an effective epitope presentation platform for study of the neutralizing antibody response in HIV-infected individuals. To address if pseudovirions can recapitulate native HIV virion epitope structures, we carefully characterized these particles, concentrating on the antigenic structure of the coreceptor binding site. By blue native gel shift assays, Gag-Env pseudovirions were shown to contain native trimers that were competent for binding to neutralizing monoclonal antibodies. In ELISA, pseudovirions exhibited increased binding of known CD4-induced antibodies following addition of CD4. Using flow cytometric analysis, fluorescently labeled pseudovirions specifically identified a subset of antigen-specific B cells in HIV-infected subjects. Interestingly, the sequence of one of these novel human antibodies, identified during cloning of single HIV-specific B cells and designated 2C6, exhibited homology to mAb 47e, a known anti-CD4-induced coreceptor binding site antibody. The secreted monoclonal antibody 2C6 did not bind monomeric gp120, but specifically bound envelope on pseudovirions. A recombinant form of the antibody 2C6 acted as a CD4-induced epitope-specific antibody in neutralization assays, yet did not bind monomeric gp120. These findings imply specificity against a quaternary epitope presented on the pseudovirion envelope spike. These data demonstrate that Gag-Env pseudovirions recapitulate CD4 and coreceptor binding pocket antigenic structures and can facilitate identification of B cell clones that secrete neutralizing antibodies. PMID:20531016

Summary All previously characterized broadly neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) target one of four major sites of vulnerability. Here, we define and structurally characterize a unique epitope on Env that is recognized by a recently discovered family of human monoclonal antibodies (PGT151-158). The PGT151 epitope is comprised of residues and glycans at the interface of gp41 and gp120 within a single protomer and glycans from both subunits of a second protomer and represents a neutralizing epitope that is dependent on both gp120 and gp41. As PGT151 binds only to properly formed, cleaved trimers, this distinctive property, and its ability to stabilize Env trimers, has enabled the successful purification of mature, cleaved Env trimers from the cell surface as a complex with PGT151. Here we compare the structural and functional properties of membrane-extracted Env trimers from several clades with those of the soluble, cleaved SOSIP gp140 trimer. PMID:24768348

A spin-1 Heisenberg model on trimerized kagome lattice is studied by doing a low-energy bosonic theory in terms of plaquette triplons defined on its triangular unit cells. The model considered has an intratriangle antiferromagnetic exchange interaction J (set to 1) and two intertriangle couplings J'>0 (nearest neighbor) and J″ (next nearest neighbor; of both signs). The triplon analysis performed on this model investigates the stability of the trimerized singlet ground state (which is exact in the absence of intertriangle couplings) in the J'-J″ plane. It gives a quantum phase diagram that has two gapless antiferromagnetically ordered phases separated by the spin-gapped trimerized singlet phase. The trimerized singlet ground state is found to be stable on J″=0 line (the nearest-neighbor case), and on both sides of it for J″≠0 , in an extended region bounded by the critical lines of transition to the gapless antiferromagnetic phases. The gapless phase in the negative J″ region has a coplanar 120∘ antiferromagnetic order with √{3 }×√{3 } structure. In this phase, all the magnetic moments are of equal length, and the angle between any two of them on a triangle is exactly 120∘. The magnetic lattice in this case has a unit cell consisting of three triangles. The other gapless phase, in the positive J″ region, is found to exhibit a different coplanar antiferromagnetic order with ordering wave vector q =(0 ,0 ) . Here, two magnetic moments in a triangle are of the same magnitude, but shorter than the third. While the angle between two short moments is 120∘-2 δ , it is 120∘+δ between a short and the long one. Only when J″=J' , their magnitudes become equal and the relative angles 120∘. The magnetic lattice in this q =(0 ,0 ) phase has the translational symmetry of the kagome lattice with triangular unit cells of reduced (isosceles) symmetry. This reduction in the point-group symmetry is found to show up as a difference in the intensities of

Two-dimensional electronic spectroscopy (2DES) was used to investigate the ultrafast energy-transfer dynamics of trimeric photosystem I of the cyanobacterium Thermosynechococcus elongatus. We demonstrate the ability of 2DES to resolve dynamics in a large pigment-protein complex containing ∼300 chromophores with both high frequency and time resolution. Monitoring the waiting-time-dependent changes of the line shape of the inhomogeneously broadened Qy(0-0) transition, we directly observe downhill energy equilibration on the 50 fs time scale. PMID:26291095

The dihydrolipoamide succinyltransferase (E2o) component of the alpha-ketoglutarate dehydrogenase complex catalyzes the transfer of a succinyl group from the S-succinyldihydrolipoyl moiety to coenzyme A. E2o is normally a 24-mer, but is found as a trimer when E2o is expressed with a C-terminal [His]6 tag. The crystal structure of the trimeric form of the catalytic domain (CD) of the Escherichia coli E2o has been solved to 3.0 A resolution using the Molecular Replacement method. The refined model contains an intact trimer in the asymmetric unit and has an R-factor of 0.257 (Rfree = 0.286) for 18,699 reflections between 10.0 and 3.0 A resolution. The core of tE2oCD (residues 187-396) superimposes onto that of the cubic E2oCD with an RMS difference of 0.4 A for all main-chain atoms. The C-terminal end of tE2oCD (residues 397-404) rotates by an average of 37 degrees compared to cubic E2oCD, disrupting the normal twofold interface. Despite the alteration of quaternary structure, the active site of tE2oCD shows no significant differences from that of the cubic E2oCD, although several side chains in the active site are more ordered in the trimeric form of E2oCD. Analysis of the available sequence data suggests that the majority of E2 components have active sites that resemble that of E. coli E2oCD. The remaining E2 components can be divided into three groups based on active-site sequence similarity. Analysis of the surface properties of both crystal forms of E. coli E2oCD suggests key residues that may be involved in the protein-protein contacts that occur between the catalytic and lipoyl domains of E2o. PMID:10739245

We present a linear-scaling method based on the use of density-functional theory (DFT) for the system-wide optimization of x-ray structural coordinates and apply it to optimize the 150 000 atoms of the photosystem-I (PS-I) trimer. The method is based on repetitive applications of a multilevel ONIOM procedure using the PW91/6-31G(d ) DFT calculations for the high level and PM3 for the lower level; this method treats all atoms in the structure equivalently, a structure in which the majority of the atoms can be considered as part of some internal "active site." To obtain a realistic single structure, some changes to the original protein model were necessary but these are kept to a minimum in order that the optimized structure most closely resembles the original x-ray one. Optimization has profound effects on the perceived electronic properties of the cofactors, with, e.g., optimization lowering the internal energy of the chlorophylls by on average 53kcalmol-1 and eliminates the enormous 115kcalmol-1 energy spread depicted by the original x-ray heavy-atom coordinates. A highly precise structure for PS-I results that is suitable for analysis of device function. Significant qualitative features of the structure are also improved such as correction of an error in the stereochemistry of one of the chlorophylls in the "special pair" of the reaction center, as well as the replacement of a water molecule with a metal cation in a critical region on the C3 axis. The method also reveals other unusual features of the structure, leading both to suggestions concerning device functionality and possible mutations between gene sequencing and x-ray structure determination. The optimization scheme is thus shown to augment the molecular modeling schemes that are currently used to add medium-resolution structural information to the raw scattering data in order to obtain atomically resolved structures. System-wide optimization is now a feasible process and its use within protein x-ray data

The preparation and characterization of a series of niobium(V) complexes that incorporate the linear-linked aryloxide trimers 2,6-bis(4,6-dimethylsalicyl)-4-tert-butylphenol [H3(Me-L)] and 2,6-bis(4-methyl-6-tert-butylsalicyl)-4-tert-butylphenol [H3(tBu-L)] are described. The chloride complex [Nb(Me-L)Cl2]2 (1) was prepared in high yield by reaction of NbCl5 with H3(Me-L) in toluene. In contrast, the analogous reaction with H3(tBu-L) gave a mixture of [Nb(tBu-L)Cl2]2 (2) and [Nb(de-tBu-L)Cl2]2 (3a). During the formation of 3a, one of tert-butyl groups at the ortho position in the tBu-L ligand was lost. When the NbCl5/H3(tBu-L) reaction was carried out in acetonitrile, Nb[H(tBu-L)]Cl3(NCMe) (4) was obtained. Heating a solution of 4 in toluene generated 2 and 3a. The isolated complex 4 underwent ligand redistribution in acetonitrile to produce Nb[H(tBu-L)]2Cl(NCMe) (5). Treatment of NbCl5 with Li3(tBu-L) in toluene afforded 2. The chloride ligands in 1 and 2 smoothly reacted with 4 equiv of MeMgI and LiStBu, resulting in [Nb(R-L)Me2]2 [R = Me (6), tBu (7)] and Nb(Me-L)(StBu)2 (8), respectively. A number of the above complexes have been characterized by X-ray crystallography. In the structures of 1, 2, and 6, the R-L ligand is bound to the metal center with a U-coordination mode, while an alternative S-conformation is adopted for 3a and 8. Complexes 4 and 5 contain a bidentate H(tBu-L) diphenoxide-monophenol ligand. PMID:12425637

Low-density membrane fragments (domains) were separated from the bulk of plasma membranes of human embryonic kidney (HEK)293 cells expressing a delta-opioid (DOP) receptor-Gi1alpha fusion protein by drastic homogenization and flotation on equilibrium sucrose density gradients. The functional activity of trimeric G proteins and capacity of the DOP receptor to stimulate both the fusion protein-linked Gi1alpha and endogenous pertussis-toxin sensitive G proteins was measured as d-Ala2, d-Leu5-enkephalin stimulated high-affinity GTPase or guanosine-5'-[gamma-35S]triphosphate ([35S]GTPgammaS) binding. The maximum d-Ala2-d-Leu5 enkephalin (DADLE)-stimulated GTPase was two times higher in low-density membrane fragments than in bulk of plasma membranes; 58 and 27 pmol/mg/min, respectively. The same difference was obtained for [35S]GTPgammaS binding. Contrarily, the low-density domains contained no more than half the DOP receptor binding sites (Bmax = 6.6 pmol/mg versus 13.6 pmol/mg). Thus, when corrected for expression levels of the receptor, low-density domains exhibited four times higher agonist-stimulated GTPase and [35S]GTPgammaS binding than the bulk plasma membranes. The regulator of G protein signaling RGS1, enhanced further the G protein functional activity but did not remove the difference between domain-bound and plasma membrane pools of G protein. The potency of the agonist in functional studies and the affinity of specific [3H]DADLE binding to the receptor were, however, the same in both types of membranes - EC50 = 4.5 +/- 0.1 x 10(-8) and 3.2 +/- 1.4 x 10(-8) m for GTPase; Kd = 1.2 +/- 0.1 and 1.3 +/- 0.1 nm for [3H]DADLE radioligand binding assay. Similar results were obtained when sodium bicarbonate was used for alkaline isolation of membrane domains. By contrast, detergent-insensitive membrane domains isolated following treatment of cells with Triton X100 exhibited no DADLE-stimulated GTPase or GTPgammaS binding. Functional coupling between the DOP receptor

Virus-like particles composed of the core antigen of hepatitis B virus (HBcAg) have been shown to be an effective platform for the display of foreign epitopes in vaccine development. Heterologous sequences have been successfully inserted at both amino and carboxy termini as well as internally at the major immunodominant epitope. We used cryogenic electron microscopy (CryoEM) and three-dimensional image reconstruction to investigate the structure of VLPs assembled from an N-terminal extended HBcAg that contained a polyhistidine tag. The insert was seen to form a trimeric spike on the capsid surface that was poorly resolved, most likely owing to it being flexible. We hypothesise that the capacity of N-terminal inserts to form trimers may have application in the development of multivalent vaccines to trimeric antigens. Our analysis also highlights the value of tools for local resolution assessment in studies of partially disordered macromolecular assemblies by cryoEM. PMID:25557498

Porins are water-filled protein channels across the outer membrane of gram-negative bacteria. They facilitate the uptake of nutrients and essential ions. Solutes are filtered by a constriction loop L3 at the mid of a pore. Porins are heat-stable and resistant to toxic agents and detergents. Most porins are trimer, but no clear explanation why trimeric form is preferable. In this work, we thus studied effects of oligomerization on porin structure and function in microscopic detail. A well-studied OmpF (general porin from Escherichia coli) and well-characterised OprP (phosphate-specific pore from Pseudomonas aeruginosa) are used as samples from 2 types of porins found in gram-negative bacteria. MD simulations of trimeric and monomeric pores in pure water and 1M NaCl solution were performed. With a salt solution, the external electric field was applied to mimic a transmembrane potential. Expectedly, OprP is more stable than OmpF. Interestingly, being a monomer turns OmpF into an anion-selective pore. The dislocation of D113's side chain on L3 in OmpF causes the disruption of cation pathway resulting in the reduction of cation influx. In contrast, OprP's structure and function are less dependent on oligomeric states. Both monomeric and trimeric OprP can maintain their anion selectivity. Our findings suggest that trimerization is crucial for both structure and function of general porin OmpF, whereas being trimer in substrate-specific channel OprP supports a pore function. PMID:26895142

The weakly bound cyclic trimer (H2O)2HBr was observed in supersonic expansion and its rotational spectrum was measured in the region 3.6-17.7 GHz by cavity Fourier-transform microwave spectroscopy. Rotational, centrifugal distortion constants, and inertial and principal hyperfine splitting constants were determined for seven isotopomers of (H2O)2HBr. In addition to the large bromine hyperfine splitting each rotational transition exhibits a fine vibrational splitting into four components, at relative intensities consistent with expectations from the G8 group classification of the vibration-rotation-tunneling motions in the trimer. The associated four low-lying states are either very close together or well below the inversion barriers, since the differences between their rotational constants are all below 0.02%. The experimental moments of inertia were used to determine rs, r0, rz, and rm(1L) geometries, in all of which the heavy atom distances are considerably shorter than similar distances in H2O-HBr and (H2O)2. An improved analysis of the measured electric dipole moment of (H2O)2HBr is reported, and all experimental results are confronted with predictions from ab initio calculations.

Based on the external and internal findings of Bhopal gas disaster victims, it was apparent that the gases and particulate matter came out as an aerosol. This was possibly the pyrolysed, reformulated, reconjugated suspension of constituents of the tank E-610 of Union Carbide India Limited, Bhopal, while it was claimed to be methyl isocyanate (MIC) only. It was postulated by the manufacturer of MIC, that the material inhaled by the victims of the Bhopal gas disaster does not cross the lung barrier (UCC press conference on 14th December 1984). It was observed that the more the victims ran, the more aerosol they inhaled and the fatalities were observed in such victims. The tissues, which were preserved in the deep freeze, were randomly selected and analysed by GC coupled with MS (ITD) Finnigan MAT, UK. 14 out of 34 autopsy cases showed MIC trimer peak in extracts of blood. This was one of the constituents of the aerosol and was also located in the tank residue, thereby proving that the trimer had passed the lung barrier. PMID:1795611

Here, we describe a new strategy that allows the rapid and efficient engineering of mono and multispecific trivalent antibodies. By fusing single-domain antibodies from camelid heavy-chain-only immunoglobulins (VHHs) to the N-terminus of a human collagen XVIII trimerization domain (TIE(XVIII)) we produced monospecific trimerbodies that were efficiently secreted as soluble functional proteins by mammalian cells. The purified VHH-TIE(XVIII) trimerbodies were trimeric in solution and exhibited excellent antigen binding capacity. Furthermore, by connecting with two additional glycine-serine-based linkers three VHH-TIE(XVIII) modules on a single polypeptide chain, we present an approach for the rational design of multispecific tandem trimerbodies with defined stoichiometry and controlled orientation. Using this technology we report here the construction and characterization of a tandem VHH-based trimerbody capable of simultaneously binding to three different antigens: carcinoembryonic antigen (CEA), epidermal growth factor receptor (EGFR) and green fluorescence protein (GFP). Multispecific tandem VHH-based trimerbodies were well expressed in mammalian cells, had good biophysical properties and were capable of simultaneously binding their targeted antigens. Importantly, these antibodies were very effective in inhibiting the proliferation of human epidermoid carcinoma A431 cells. Multispecific VHH-based trimerbodies are therefore ideal candidates for future applications in various therapeutic areas. PMID:27345490

We use nonperturbative linked-cluster expansions to determine the ground-state energy per site of the spin-one Heisenberg model on the kagome lattice. To this end, a parameter is introduced allowing us to interpolate between a fully trimerized state and the isotropic model. The ground-state energy per site of the full graph decomposition up to graphs of six triangles (18 spins) displays a complex behavior as a function of this parameter close to the isotropic model which we attribute to divergencies of partial series in the graph expansion of quasi-1D unfrustrated chain graphs. More concretely, these divergencies can be traced back to a quantum critical point of the one-dimensional unfrustrated chain of coupled triangles. Interestingly, the reorganization of the nonperturbative linked-cluster expansion in terms of clusters with enhanced symmetry yields a ground-state energy per site of the isotropic two-dimensional model that is in quantitative agreement with other numerical approaches in favor of a spontaneous trimerization of the system. Our findings are of general importance for any nonperturbative linked-cluster expansion on geometrically frustrated systems.

Here, we describe a new strategy that allows the rapid and efficient engineering of mono and multispecific trivalent antibodies. By fusing single-domain antibodies from camelid heavy-chain-only immunoglobulins (VHHs) to the N-terminus of a human collagen XVIII trimerization domain (TIEXVIII) we produced monospecific trimerbodies that were efficiently secreted as soluble functional proteins by mammalian cells. The purified VHH-TIEXVIII trimerbodies were trimeric in solution and exhibited excellent antigen binding capacity. Furthermore, by connecting with two additional glycine-serine-based linkers three VHH-TIEXVIII modules on a single polypeptide chain, we present an approach for the rational design of multispecific tandem trimerbodies with defined stoichiometry and controlled orientation. Using this technology we report here the construction and characterization of a tandem VHH-based trimerbody capable of simultaneously binding to three different antigens: carcinoembryonic antigen (CEA), epidermal growth factor receptor (EGFR) and green fluorescence protein (GFP). Multispecific tandem VHH-based trimerbodies were well expressed in mammalian cells, had good biophysical properties and were capable of simultaneously binding their targeted antigens. Importantly, these antibodies were very effective in inhibiting the proliferation of human epidermoid carcinoma A431 cells. Multispecific VHH-based trimerbodies are therefore ideal candidates for future applications in various therapeutic areas. PMID:27345490

We reported here for the first time on the use of cotton thread combined with novel gold nanoparticle trimer reporter probe for low-cost, sensitive and rapid detection of a lung cancer related biomarker, human ferritin. A model system comprising ferritin as an analyte and a pair of monoclonal antibodies was used to demonstrate the proof-of-concept on the dry-reagent natural cotton thread immunoassay device. Results indicated that the using of novel gold nanoparticle trimer reporter probe greatly improved the sensitivity comparing with traditional gold nanoparticle reporter probe on the cotton thread immunoassay device. The assay avoids multiple incubation and washing steps performed in most conventional protein analyses. Although qualitative tests are realized by observing the color change of the test zone, quantitative data are obtained by recording the optical responses of the test zone with a commercial scanner and corresponding analysis software. Under optimal conditions, the cotton thread immunoassay device was capable of measuring 10 ng/mL human ferritin under room temperature which is sensitive enough for clinical diagnosis. Moreover, the sample solution employed in the assays is just 8 μL, which is much less than traditional lateral flow strip based biosensors. PMID:26343440

The magnetization process, the susceptibility, and the specific heat of the spin- 1/2 antiferromagnet (AF)-AF-ferromagnet (F) and F-F-AF trimerized quantum Heisenberg chains have been investigated by means of the transfer matrix renormalization group (TMRG) technique as well as the modified spin-wave (MSW) theory. A magnetization plateau at m=1/6 for both trimerized chains is observed at low temperature. The susceptibility and the specific heat show various behaviors for different ferromagnetic and antiferromagnetic interactions and in different magnetic fields. The TMRG results of susceptibility and the specific heat can be nicely fitted by a linear superposition of double two-level systems, where two fitting equations are proposed. Three branch excitations, one gapless excitation and two gapful excitations, for both systems are found within the MSW theory. It is observed that the MSW theory captures the main characteristics of the thermodynamic behaviors at low temperatures. The TMRG results are also compared with the possible experimental data.

Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, from the Latin dirigere, to guide or align). The first three-dimensional structure of a DP ((+)-pinoresinol-forming DP, 1.95 Å resolution, rhombohedral space group H32)) is reported herein. It has a tightly packed trimeric structure with an eight-stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcohol radicals or a radical and a monolignol). Interestingly, there are six differentially conserved residues in DPs affording either the (+)- or (−)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition. PMID:25411250

Based on the ethnopharmacological data showing that either wild bilberry leaves or whole aerial parts of the plants have been used as antidiabetic drugs, it can be hypothesized that the controversial results of various clinical and animal investigations may be caused by different contents of the active principles in different aerial parts of the bilberry/blueberry (Vaccinium spp.) plants, as well as by their geographical and seasonal variability. The aim of this study was to compare the content of procyanidin type A- and -B trimers in different parts of wild bilberry (Vaccinium myrtillus L.) and northern highbush blueberry (V. corymbosum L.) cultivars. Stems (60 samples) and leaves (30 samples) of wild bilberries and northern highbush blueberry cultivars 'Ama' and 'North Blue' were collected at different locations in Estonia around the year, and analyzed for the concentration of the target polyphenols by HPLC-MS/MS. The highest content of type A doubly linked trimer, a known antidiabetic substance, was established in the stems of V. myrtillus. These contained up to 100 times more of the active substance than the leaves of V. myrtillus and at least 1000 times more than the leaves of V. corymbosum, whereas the seasonal/geographical variation was nearly tenfold. We suggest using stems of V. myrtillus for future animal and clinical investigations of bilberry preparations against diabetes. PMID:25115086

In the present paper, the formation of stable hydrated (H2SO4)3(H2O)n clusters has been studied using the Density Functional Theory (DFT) at PW91PW91/6-311++(3df,3pd) level. We have found that the hydration of H2SO4 trimers is stronger than that of H2SO4 dimers and tends to decrease at large hydration numbers. We have shown that the affinity of H2SO4 to (H2SO4)2(H2O)n is much higher than that H2SO4 to (H2SO4) (H2O)n. We have compared the equilibrium constants of H2O-mediated trimerization of H2SO4 obtained using PW91PW91/6-311++(3df,3pd) method with experimental data and found that theory and experimentation are in good agreement. The new thermochemical data can be used in a wide range of nucleation studies and can be utilized for the development of quantum-based models of nucleation rates.

Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, from the Latin dirigere, to guide or align). The first three-dimensional structure of a DP ((+)-pinoresinol-forming DP, 1.95 Å resolution, rhombohedral space group H32)) is reported herein. It has a tightly packed trimeric structure with an eight-stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcoholmore » radicals or a radical and a monolignol). Interestingly, there are six differentially conserved residues in DPs affording either the (+)- or (₋)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. We find DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition.« less

Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, from the Latin dirigere, to guide or align). The first three-dimensional structure of a DP ((+)-pinoresinol-forming DP, 1.95 Å resolution, rhombohedral space group H32)) is reported herein. It has a tightly packed trimeric structure with an eight-stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcohol radicals or a radical and a monolignol). Interestingly, there are six differentially conserved residues in DPs affording either the (+)- or (₋)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. We find DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition.

The insecticidal feature of the three-domain Cry δ-endotoxins from Bacillus thuringiensis is generally attributed to their capability to form oligomeric pores, causing lysis of target larval midgut cells. However, the molecular description of their oligomerization process has not been clearly defined. Here a stable prepore of the 65-kDa trypsin-activated Cry4Ba mosquito-specific toxin was established through membrane-mimetic environments by forming an ∼200-kDa octyl-β-D-glucoside micelle-induced trimer. The SDS-resistant trimer caused cytolysis to Sf9 insect cells expressing Aedes-mALP (a Cry4Ba receptor) and was more effective than a toxin monomer in membrane perturbation of calcein-loaded liposomes. A three-dimensional model of toxin trimer obtained by negative-stain EM in combination with single-particle reconstruction at ∼5 nm resolution showed a propeller-shaped structure with 3-fold symmetry. Fitting the three-dimensional reconstructed EM map with a 100-ns molecular dynamics-simulated Cry4Ba structure interacting with an octyl-β-D-glucoside micelle showed relative positioning of individual domains in the context of the trimeric complex with a major protrusion from the pore-forming domain. Moreover, high-speed atomic force microscopy imaging at nanometer resolution and a subsecond frame rate demonstrated conformational transitions from a propeller-like to a globularly shaped trimer upon lipid membrane interactions, implying prepore-to-pore conversion. Real-time trimeric arrangement of monomers associated with L-α-dimyristoylphosphatidylcholine/3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonic acid bicelle membranes was also envisaged by successive high-speed atomic force microscopy imaging, depicting interactions among three individual subunits toward trimer formation. Together, our data provide the first pivotal insights into the structural requirement of membrane-induced conformational changes of Cry4Ba toxin monomers for the

Aim: Cinnamon extracts rich in procyanidin oligomers have shown to improve pancreatic β-cell function in diabetic db/db mice. The aim of this study was to identify the active compounds in extracts from two species of cinnamon responsible for the pancreatic β-cell protection in vitro. Methods: Cinnamon extracts were prepared from Cinnamomum tamala (CT-E) and Cinnamomum cassia (CC-E). Six compounds procyanidin B2 (cpd1), (−)-epicatechin (cpd2), cinnamtannin B1 (cpd3), procyanidin C1 (cpd4), parameritannin A1 (cpd5) and cinnamtannin D1 (cpd6) were isolated from the extracts. INS-1 pancreatic β-cells were exposed to palmitic acid (PA) or H2O2 to induce lipotoxicity and oxidative stress. Cell viability and apoptosis as well as ROS levels were assessed. Glucose-stimulated insulin secretion was examined in PA-treated β-cells and murine islets. Results: CT-E, CC-E as well as the compounds, except cpd5, did not cause cytotoxicity in the β-cells up to the maximum dosage using in this experiment. CT-E and CC-E (12.5–50 μg/mL) dose-dependently increased cell viability in both PA- and H2O2-treated β-cells, and decreased ROS accumulation in H2O2-treated β-cells. CT-E caused more prominent β-cell protection than CC-E. Furthermore, CT-E (25 and 50 μg/mL) dose-dependently increased glucose-stimulated insulin secretion in PA-treated β-cells and murine islets, but CC-E had little effect. Among the 6 compounds, trimer procyanidins cpd3, cpd4 and cpd6 (12.5–50 μmol/L) dose-dependently increased the cell viability and decreased ROS accumulation in H2O2-treated β-cells. The trimer procyanidins also increased glucose-stimulated insulin secretion in PA-treated β-cells. Conclusion: Trimer procyanidins in the cinnamon extracts contribute to the pancreatic β-cell protection, thus to the anti-diabetic activity. PMID:27238208

The major light harvesting complex II (LHCII) of green plants plays a key role in the absorption of sunlight, the regulation of photosynthesis, and in preventing photodamage by excess light. The latter two functions are thought to involve the lumenal loop and the N-terminal domain. Their structure and mobility in an aqueous environment are only partially known. Electron paramagnetic resonance (EPR) has been used to measure the structure of these hydrophilic protein domains in detergent-solubilized LHCII. A new technique is introduced to prepare LHCII trimers in which only one monomer is spin-labeled. These heterogeneous trimers allow to measure intra-molecular distances within one LHCII monomer in the context of a trimer by using double electron-electron resonance (DEER). These data together with data from electron spin echo envelope modulation (ESEEM) allowed to model the N-terminal protein section, which has not been resolved in current crystal structures, and the lumenal loop domain. The N-terminal domain covers only a restricted area above the superhelix in LHCII, which is consistent with the "Velcro" hypothesis to explain thylakoid grana stacking (Standfuss, J., van Terwisscha Scheltinga, A. C., Lamborghini, M., and Kühlbrandt, W. (2005) EMBO J. 24, 919-928). The conformation of the lumenal loop domain is surprisingly different between LHCII monomers and trimers but not between complexes with and without neoxanthin bound. PMID:26316535

A method of test for residual isophorone diisocyanate (IPDI) trimer in experimental formulation polyester-polyurethane (PEPU) thermoset coatings on metal food packaging is described. The method involves extraction of coated panels using acetonitrile containing dibutylamine for concurrent derivatisation, and then high performance liquid chromatography with electrospray ionisation tandem mass spectrometric detection (LC-MS/MS). Single laboratory validation was carried out using three different experimental PEPU-based coatings. The calibrations were linear, the analytical recovery was good, no interferences were seen, and substance identification criteria were met. The detection limit of the method is around 0.02 micro g/100 cm(2) of coating, which for a typical sized can and assuming complete migration of any residual IPDI trimer, corresponds to about 0.2 micro g/kg food or beverage. Separate studies indicated that, even if migration occurred at such low levels, the IPDI trimer would not be expected to persist in canned aqueous or fatty foodstuffs as it would hydrolyse to the corresponding aliphatic amine or react with food components to destroy the isocyanate moiety. The method of test developed here for residual IPDI trimer in thermoset polyester-polyurethane coatings should prove to be a valuable tool for investigating the cure kinetics of these novel coatings and help to guide the development of enhanced formulations. PMID:17178416

In this study, we show a 1:1:1 stoichiometry between the three Arabidopsis thaliana secondary cell wall isozymes: CESA4, CESA7, and CESA8. This ratio was determined utilizing a simple but elegant method of quantitative immunoblotting using isoform-specific antibodies and 35S-labeled protein standards for each CESA. Additionally, the observed equimolar stoichiometry was found to be fixed along the axis of the stem, which represents a developmental gradient. Our results complement recent spectroscopic analyses pointing toward an 18-chain cellulose microfibril. Taken together, we propose that the CSC is composed of a hexamer of catalytically active CESA trimers, with each CESA in equimolar amounts. This finding is a crucial advance in understanding how CESAs integrate to form higher order complexes, which is a key determinate of cellulose microfibril and cell wall properties.

Bowl-shaped macrocycles have the distinctive feature that their two sides are differentiated, and thus can be developed into elaborate hosts that fix a target molecule in a controlled geometry through multipoint interactions. We now report the synthesis of a bowl-shaped macrocyclic trimer of the boron-dipyrrin (BODIPY) complex and its unidirectional threading of guest molecules. Six polarized B(δ+) -F(δ-) bonds are directed towards the center of the macrocycle, which enables strong recognition of cationic guests. Specifically, the benzylbutylammonium ion is bound in a manner in which the benzyl group is located at the convex face of the bowl and the butyl group at its concave face. Furthermore, adrenaline was strongly captured on the convex side of the bowl by hydrogen bonding, Coulomb forces, and C-H⋅⋅⋅π interactions. PMID:27351597

The Poisson-TrEsp method (where TrEsp stands for transition charges from electrostatic potentials) has been successfully applied to calculate excitonic couplings in a variety of pigment-protein complexes. It relies on an isomorphism that allows for relating the excitonic coupling between transition densities in dielectric media to their Coulomb coupling. This isomorphism was derived by Hsu et al. (J. Chem. Phys. 114, 3065, (2001)) using time-dependent density functional response theory. In this article, we provide an alternative and simple derivation by first-order perturbation theory. An application of Poisson-TrEsp to photosystem I trimers reveals that the local field correction/screening factor depends on the mutual orientation of the pigments and on the dielectric boundaries rather than on distance. A mean correction factor of f = 0.69 is determined for this system. PMID:21912923

ABSTRACT Chikungunya virus (CHIKV) is a reemerging alphavirus that causes a debilitating arthritic disease and infects millions of people and for which no specific treatment is available. Like many alphaviruses, the structural targets on CHIKV that elicit a protective humoral immune response in humans are poorly defined. Here we used phage display against virus-like particles (VLPs) to isolate seven human monoclonal antibodies (MAbs) against the CHIKV envelope glycoproteins E2 and E1. One MAb, IM-CKV063, was highly neutralizing (50% inhibitory concentration, 7.4 ng/ml), demonstrated high-affinity binding (320 pM), and was capable of therapeutic and prophylactic protection in multiple animal models up to 24 h postexposure. Epitope mapping using a comprehensive shotgun mutagenesis library of 910 mutants with E2/E1 alanine mutations demonstrated that IM-CKV063 binds to an intersubunit conformational epitope on domain A, a functionally important region of E2. MAbs against the highly conserved fusion loop have not previously been reported but were also isolated in our studies. Fusion loop MAbs were broadly cross-reactive against diverse alphaviruses but were nonneutralizing. Fusion loop MAb reactivity was affected by temperature and reactivity conditions, suggesting that the fusion loop is hidden in infectious virions. Visualization of the binding sites of 15 different MAbs on the structure of E2/E1 revealed that all epitopes are located at the membrane-distal region of the E2/E1 spike. Interestingly, epitopes on the exposed topmost and outer surfaces of the E2/E1 trimer structure were neutralizing, whereas epitopes facing the interior of the trimer were not, providing a rationale for vaccine design and therapeutic MAb development using the intact CHIKV E2/E1 trimer. IMPORTANCE CHIKV is the most important alphavirus affecting humans, resulting in a chronic arthritic condition that can persist for months or years. In recent years, millions of people have been infected

A major advance in the search for an HIV vaccine has been the development of a near-native Envelope trimer (BG505 SOSIP.664) that can induce robust autologous Tier 2 neutralization. Here, potently neutralizing monoclonal antibodies (nAbs) from rabbits immunized with BG505 SOSIP.664 are shown to recognize an immunodominant region of gp120 centered on residue 241. Residue 241 occupies a hole in the glycan defenses of the BG505 isolate, with fewer than 3% of global isolates lacking a glycan site at this position. However, at least one conserved glycan site is missing in 89% of viruses, suggesting the presence of glycan holes in most HIV isolates. Serum evidence is consistent with targeting of holes in natural infection. The immunogenic nature of breaches in the glycan shield has been under-appreciated in previous attempts to understand autologous neutralizing antibody responses and has important potential consequences for HIV vaccine design. PMID:27545891

Polarized transient absorption spectroscopy has been applied to study the carotenoid to chlorophyll excitation energy transfer in the trimeric fucoxanthin-chlorophyll protein FCPa of the centric diatom Cyclotella meneghiniana. We examined the transfer pathways after excitation in the main carotenoid band (S 0 → S 2 transition) with two excitation wavelengths that address either red fucoxanthins only or blue fucoxanthins and the xanthophyll cycle pigments. We were able to identify different transition dipole moments for the S 1 and the ICT state, which are assumed to be a single coupled state that transfers excitation energy to chlorophyll a. Furthermore we obtained different transition dipole moments for the first excited state S 1 of fucoxanthin depending on the excitation wavelength.

We revisit the singlet-triplet energy gap (ΔE(ST)) of silicon trimer and evaluate the gaps of its derivatives by attachment of a cation (H(+), Li(+), Na(+), and K(+)) using the wavefunction-based methods including the composite G4, coupled-cluster theory CCSD(T)/CBS, CCSDT and CCSDTQ, and CASSCF/CASPT2 (for Si3) computations. Both (1)A1 and (3)A2' states of Si3 are determined to be degenerate. An intersystem crossing between both states appears to be possible at a point having an apex bond angle of around α = 68 ± 2° which is 16 ± 4 kJ/mol above the ground state. The proton, Li(+) and Na(+) cations tend to favor the low-spin state, whereas the K(+) cation favors the high-spin state. However, they do not modify significantly the ΔE(ST). The proton affinity of silicon trimer is determined as PA(Si3) = 830 ± 4 kJ/mol at 298 K. The metal cation affinities are also predicted to be LiCA(Si3) = 108 ± 8 kJ/mol, NaCA(Si3) = 79 ± 8 kJ/mol and KCA(Si3) = 44 ± 8 kJ/mol. The chemical bonding is probed using the electron localization function, and ring current analyses show that the singlet three-membered ring Si3 is, at most, nonaromatic. Attachment of the proton and Li(+) cation renders it anti-aromatic. PMID:25694392

The development of a preventive vaccine against human immunodeficiency virus (HIV-1) infection is the most efficient method to control the epidemic. The ultimate goal is to develop a vaccine able to induce specific neutralizing, non-neutralizing antibodies and cellular mediated immunity (CMI). Humoral and CMI responses can be directed to glycoproteins that are normally presented as a trimeric spike on the virus surface (gp140). Despite safer, subunit vaccines are normally less immunogenic/effective and need to be delivered together with an adjuvant. The choice of a suitable adjuvant can induce effective humoral and CMI that utterly lead to full protection against disease. In this report, we established a hierarchy of adjuvant potency on humoral and CMI when admixed with the recombinant HIV gp140 trimer. We show that vaccination with gp140 in the presence of different adjuvants can induce high-affinity antibodies, follicular helper T cells and germinal center B cells. The data show that poly (I:C) is the most potent adjuvant to induce specific CMI responses evidenced by IFN-γ production and CD4+/CD8+ T cell proliferation. Furthermore, we demonstrate that combining some adjuvants like MPL plus Alum and MPL plus MDP exert additive effects that impact on the magnitude and quality of humoral responses while mixing MDP with poly (I:C) or with R848 had no impact on total IgG titers but highly impact IgG subclass. In addition, heterologous DNA prime- protein boost yielded higher IgG titers when compare to DNA alone and improved the quality of humoral response when compare to protein immunization as evidenced by IgG1/IgG2a ratio. The results presented in this paper highlight the importance of selecting the correct adjuvant-antigen combination to potentiate desired cells for optimal stimulation. PMID:26727218

1,3,5-Trioxane-2,4,6-trione (cyclic trimer of CO2) is the product of a four-step synthesis: chlorination of isobutyraldehyde; cyclotrimerization of 2-chloro-2-methylpropanal; dehydochlorination of 2,4,6-tris(2-chloropropan)-2-yl-1,3,5-trioxane; ozonolysis at -80 °C of 2,4,6-tri(propan-2-ylidene)-1,3,5-trioxane. This trioxane-trione is detected in solution at temperatures between -80 to -40 °C, and its conversion to CO2 is monitored by (13)C NMR and FTIR. The CO2 trimer has a half-life of approximately 40 min at -40 °C. PMID:27183100

The Fenna-Matthews-Olson (FMO) trimer (composed of identical subunits) from the green sulfur bacterium Chlorobaculum tepidum is an important protein model system to study exciton dynamics and excitation energy transfer (EET) in photosynthetic complexes. In addition, FMO is a popular model for excitonic calculations, with many theoretical parameter sets reported describing different linear and nonlinear optical spectra. Due to fast exciton relaxation within each subunit, intermonomer EET results predominantly from the lowest energy exciton states (contributed to by BChl a 3 and 4). Using experimentally determined shapes for the spectral densities, simulated optical spectra are obtained for the entire FMO trimer. Simultaneous fits of low-temperature absorption, fluorescence, and hole-burned spectra place constraints on the determined pigment site energies, providing a new Hamiltonian that should be further tested to improve modeling of 2D electronic spectroscopy data and our understanding of coherent and dissipation effects in this important protein complex. PMID:27438068

Neisseria meningitidis NhhA (Neisseria hia/hsf homologue A) is an oligomeric outer membrane protein belonging to the family of trimeric autotransporter adhesins. NhhA mediates the interaction of N. meningitidis with human epithelial cells and components of the extracellular matrix. The recombinant protein is able to induce bactericidal antibodies and hence has also been considered a potential vaccine candidate. In this study, we analyzed the production of NhhA in a large panel of N. meningitidis strains belonging to different serogroups and clonal complexes. We found that trimeric NhhA was produced at different levels by the various strains tested. In some strains belonging to the clonal complex ST41/44, the protein is detectable only as a monomer. Sequencing of the nhhA gene and generation of complementing strains in different genetic backgrounds have proved that a single mutation (Gly to Asp) in the translocator domain affected both trimerization and surface localization of NhhA. In vitro infection assays showed that this mutation impairs meningococcal NhhA-mediated adhesion, suggesting that strains carrying the mutation may rely on different strategies or molecules to mediate interaction with host cells. Finally, we demonstrated that N. meningitidis ST41/44 strains producing the mutated form did not induce killing mediated by NhhA-specific bactericidal antibodies. Our data help to elucidate the secretion mechanisms of trimeric autotransporters and to understand the contribution of NhhA in the evolutionary process of host-Neisseria interactions. Also, they might have important implications for the evaluation of NhhA as a vaccine candidate. PMID:21844231

The native, functional HIV-1 envelope glycoprotein (Env) complex is a trimer of two non-covalently associated subunits: the gp120 surface glycoprotein and the gp41 transmembrane glycoprotein. However, various non-functional forms of Env are present on virus particles and HIV-1-infected cells, some of which probably arise as the native complex decays. The aberrant forms include gp120-gp41 monomers and oligomers, as well as gp41 subunits from which gp120 has dissociated. The presence of non-functional Env creates binding sites for antibodies that do not recognize native Env complexes and that are, therefore, non-neutralizing. Non-native Env forms (monomers, dimers, tetramers and aggregates) can also arise when soluble gp140 proteins, lacking the cytoplasmic and transmembrane domains of gp41, are expressed for vaccine studies. We recently identified five amino acids in the gp41 N-terminal region (I535, Q543, S553, K567 and R588) that promote gp140 trimerization. We have now studied their influence on the function and antigenic properties of JR-FL Env expressed on the surfaces of pseudoviruses and Env-transfected cells. The 5 substitutions in gp41 reduce the expression of non-trimeric gp160s, without affecting trimer levels. Pseudovirions bearing the mutant Env are fully infectious with similar kinetics of Env-mediated fusion. Various non-neutralizing antibodies bind less strongly to the Env mutant, but neutralizing antibody binding is unaffected. Hence the gp41 substitutions do not adversely affect Env structure, supporting their use for making new Env-based vaccines. The mutant Env might also help in studies intended to correlate antibody binding to virus neutralization. Of note is that the 5 residues are much more frequent, individually or collectively, in viruses from subtypes other than B.

Adiponectin is a circulating insulin-sensitizing hormone that homooligomerizes into trimers, hexamers, and higher molecular weight (HMW) species. Low levels of circulating HMW adiponectin appear to increase the risk for insulin resistance. Currently, assembly of adiponectin oligomers and, consequently, mechanisms responsible for decreased HMW adiponectin in insulin resistance are not well understood. In the work reported here, we analyzed the reassembly of the most abundant HMW adiponectin species, the octadecamer, following its collapse to smaller oligomers in vitro. Purified bovine serum adiponectin octadecamer was treated with reducing agents at pH 5 to obtain trimers. These reduced trimers partially and spontaneously reassembled into octadecamers upon oxidative formation of disulfide bonds. Disulfide bonds appear to occupy a greater role in the process of oligomerization than in the structural stabilization of mature octadecamer. Stable octadecamers lacking virtually all disulfide bonds could be observed in abundance using native gel electrophoresis, dynamic light scattering, and collision-induced dissociation nanoelectrospray ionization mass spectrometry. These findings indicate that while disulfide bonds help to maintain the mature octadecameric adiponectin structure, their more important function is to stabilize intermediates during the assembly of octadecamer. Adiponectin oligomerization must proceed through intermediates that are at least partially reduced. Accordingly, fully oxidized adiponectin hexamers failed to reassemble into octadecamers at a rate comparable to that of reduced trimers. As the findings from the present study are based on in vitro experiments, their in vivo relevance remains unclear. Nevertheless, they describe a redox environment-dependent model of adiponectin oligomerization that can be tested using cell-based approaches. PMID:19943704

The conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41 is transiently exposed during the fusion process by forming a pre-hairpin intermediate, thus representing an attractive target for the design of fusion inhibitors and neutralizing antibodies. In previous studies we reported a series of broadly neutralizing mini-antibodies derived from a synthetic naive human combinatorial antibody library by panning against a mimetic of the trimeric N-HR coiled coil, followed by affinity maturation using targeted diversification of the CDR-H2 loop. Here we report crystal structures of the N-HR mimetic 5-Helix with two Fabs that represent the extremes of this series: Fab 8066 is broadly neutralizing across a wide panel of B and C type HIV-1 viruses, whereas Fab 8062 is non-neutralizing. The crystal structures reveal important differences in the conformations of the CDR-H2 loops in the complexes that propagate into other regions of the antigen-antibody interface, and suggest that both neutralization properties and affinity for the target can be attributed, at least in part, to the differences in the interactions of the CDR-H2 loops with the antigen. Furthermore, modeling of the complex of an N-HR trimer with three Fabs suggests that the CDR-H2 loop may be involved in close intermolecular contacts between neighboring antibody molecules, and that such contacts may hinder the formation of complexes between the N-HR trimer and more than one antibody molecule depending on the conformation of the bound CDR-H2 loop which is defined by its interactions with antigen. Comparison with the crystal structure of the complex of 5-Helix with another neutralizing monoclonal antibody known as D5, derived using an entirely different antibody library and panning procedure, reveals remarkable convergence in the optimal sequence and conformation of the CDR-H2 loop.

Nonphotochemical hole-burned spectra obtained as a function of burn wavelength at 4.2 K are reported for the isolated LHC II peripheral antenna complex of photosystem II. The lowest-energy state of the trimer complex is shown to lie at 680 nm, 4 nm below the most intense Chl a band at 676 nm. The linear electron-phonon coupling for the 680-nm state is characterized and used to predict that its fluorescence origin should lie at 681 nm, precisely coincident with the observed origin at 4.2 K. The 680-nm band carries the equivalent absorption strength of about one chlorophyll a molecule per C[sub 3] trimer complex, which contains about 27 chlorophyll a molecules. The 680-nm absorption band possesses an inhomogeneous width of [approximately] 120 cm[sup [minus]1], and its zero-phonon line distribution function is largely uncorrelated with those of the higher-energy states. Zero-phonon hole widths are used to determine that the fluorescent 680-nm state dephases in 10 ps at 4.2 K. An interpretation of this dephasing is given in terms of the trimer of subunits structure. Based on the satellite hole structure observed upon hole burning into the 680-nm state, two new states at 674 and 678 nm are identified. 56 refs., 5 figs.

Human cytomegalovirus encodes at least 25 membrane glycoproteins that are found in the viral envelope(1). While gB represents the fusion protein, two glycoprotein complexes control the tropism of the virus: the gHgLgO trimer is involved in the infection of fibroblasts, and the gHgLpUL128L pentamer is required for infection of endothelial, epithelial and myeloid cells(2-5). Two reports suggested that gB binds to ErbB1 and PDGFRα (refs 6,7); however, these results do not explain the tropism of the virus and were recently challenged(8,9). Here, we provide a 19 Å reconstruction for the gHgLgO trimer and show that it binds with high affinity through the gO subunit to PDGFRα, which is expressed on fibroblasts but not on epithelial cells. We also provide evidence that the trimer is essential for viral entry in both fibroblasts and epithelial cells. Furthermore, we identify the pentamer, which is essential for infection of epithelial cells, as a trigger for the ErbB pathway. These findings help explain the broad tropism of human cytomegalovirus and indicate that PDGFRα and the viral gO subunit could be targeted by novel anti-viral therapies. PMID:27573107

A new ternary van der Waals complex of the type rare gas-rare gas-linear molecule, ArNeN2O, was investigated using a pulsed molecular beam cavity Fourier transform microwave spectrometer. The rotational spectra of six isotopomers of the trimer were studied in detail. These include Ar20Ne- 14N14NO, Ar22Ne- 14N14NO, Ar20Ne-15N14NO, Ar22Ne- 15N14NO, Ar20Ne- 14N15NO and Ar22Ne- 14N15NO. Nuclear quadrupole hyperfine structures of the rotational transitions that are due to the one or two 14N nuclei were resolved and analysed. The resulting spectroscopic constants were used to provide structural and dynamical information about the trimer. Based on the quartic centrifugal distortion constants, a harmonic force field analysis was performed to estimate the frequencies of the van der Waals vibrational modes. A perturbation of the electronic charge distribution at the site of the central 14N nucleus of N2O upon complex formation was detected and discussed. Differences of structural parameters of the trimer as compared to those of the respective dimer units are indicative of the presence of significant three-body non-additive contributions to the interaction energy.

The induction of the isiA (CP43') protein in iron-stressed cyanobacteria is accompanied by the formation of a ring of 18 CP43' proteins around the photosystem I (PSI) trimer and is thought to increase the absorption cross section of PSI within the CP43'-PSI supercomplex. In contrast to these in vitro studies, our in vivo measurements failed to demonstrate any increase of the PSI absorption cross section in two strains (Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803) of iron-stressed cells. We report that iron-stressed cells exhibited a reduced capacity for state transitions and limited dark reduction of the plastoquinone pool, which accounts for the increase in PSII-related 685 nm chlorophyll fluorescence under iron deficiency. This was accompanied by lower abundance of the NADP-dehydrogenase complex and the PSI-associated subunit PsaL, as well as a reduced amount of phosphatidylglycerol. Nondenaturating polyacrylamide gel electrophoresis separation of the chlorophyll-protein complexes indicated that the monomeric form of PSI is favored over the trimeric form of PSI under iron stress. Thus, we demonstrate that the induction of CP43' does not increase the PSI functional absorption cross section of whole cells in vivo, but rather, induces monomerization of PSI trimers and reduces the capacity for state transitions. We discuss the role of CP43' as an effective energy quencher to photoprotect PSII and PSI under unfavorable environmental conditions in cyanobacteria in vivo. PMID:16798943

We present a novel protein crystallization strategy, applied to the crystallization of human T cell leukemia virus type 1 (HTLV-1) transmembrane protein gp21 lacking the fusion peptide and the transmembrane domain, as a chimera with the Escherichia coli maltose binding protein (MBP). Crystals could not be obtained with a MBP/gp21 fusion protein in which fusion partners were separated by a flexible linker, but were obtained after connecting the MBP C-terminal alpha-helix to the predicted N-terminal alpha-helical sequence of gp21 via three alanine residues. The gp21 sequences conferred a trimeric structure to the soluble fusion proteins as assessed by sedimentation equilibrium and X-ray diffraction, consistent with the trimeric structures of other retroviral transmembrane proteins. The envelope protein precursor, gp62, is likewise trimeric when expressed in mammalian cells. Our results suggest that MBP may have a general application for the crystallization of proteins containing N-terminal alpha-helical sequences. PMID:9684894

Calculations of vibrational energies and rotational constants are carried out for the van der Waals trimer Ar[sub 2]-HF. The calculations include all five intermolecular degrees of freedom. The different intramolecular vibrational states [ital v] of the HF molecule are separated out adiabatically, so that the calculations are carried out on effective intermolecular potentials for each HF vibrational state separately. Calculations are performed both on pairwise-additive potentials, derived from the well-known Ar-Ar and Ar-HF potentials, and on nonadditive potentials, incorporating various different contributions to the three-body forces. The results are compared with experimental results from high-resolution spectroscopy, and provide detailed information on the anisotropy of the nonadditive intermolecular forces. As in previous work on Ar[sub 2]-HCl, it is found that a very important nonadditive term arises from the interaction between the permanent multipoles of the HF molecule and the exchange quadrupole caused by distortion of the two Ar atoms as they overlap. An improved model of this term is described.

Five potential charge transfer complexes of trimeric perfluoro-o-phenylene mercury (I) with tetrathiafulvalene (TTF) and tetramethyltetraselenefulvalene (TMTSF) were grown from different solvent mixtures. The adducts (I)2·TTF (1) and I·TTF (2) were grown by slow evaporation from the 1:1 mixture of dichloromethane (CH2Cl2, DCM) and carbon disulfide (CS2). Use of the different 1:1 solvent mixtures of dichloromethane (CH2Cl2, DCM) and dichloroethane (C2H4Cl2, DCE) has led to the crystalline adducts I·TTF (3) and I·TTF·DCE (4). Adduct I.TMTSF (5) was grown by the interface crystallization on the border of two immiscible layers, ethyl acetate, and carbon disulfide. The cocrystals differ by the donor–acceptor ratio, molecular packing, and the solvent inclusion. The components in 1–5 form mixed donor–acceptor stacks. The stacks are stabilized by Hg···S and Hg···C short contacts, while the lateral interactions between stacks include F···F, CH···F, and S/Se···F short contacts.

Phytochemical investigation of the ethyl acetate fraction of the methanol extract of the leaves of Ixora coccinea led to the isolation and identification of an A-type trimeric proanthocyanidin epicatechin-(2β→O→7, 4β→8)-epicatechin-(5→O→2β, 6→4β)-epicatechin named ixoratannin A-2 along with seven known compounds, epicatechin, procyanidin A2, cinnamtannin B-1, and four flavon-3-ol rhamnosides viz: kaempferol-7-O-α-L-rhamnnoside, kaempferol-3-O-α-L-rhamnoside, quercetin-3-O-α-L-rhamnopyranoside, and kaempferol-3,7-O-α-L-dirhamnoside. The structures were elucidated by the application of IR, UV, MS, 1D-, and 2D-NMR spectroscopic analyses and by comparison with literature data. Antioxidant evaluation of isolated compounds revealed that ixoratannin A-2 and cinnamtannin B-1 were the most active compounds in DPPH, inhibition of lipid peroxidation and nitric oxide radical scavenging assays. Antibacterial activities were assessed by means of agar-diffusion assays using Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa and Bacillus subtilis. All tested compounds inhibited the growth of B. subtilis, while only epicatechin and quercetin-3-O-α-L-rhamnopyranoside inhibited the growth of E. coli. PMID:20843529

Phase transitions that occur in materials, driven, for instance, by changes in temperature or pressure, can dramatically change the materials' properties. Discovering new types of transitions and understanding their mechanisms is important not only from a fundamental perspective, but also for practical applications. Here we investigate a recently discovered Fe4O5 that adopts an orthorhombic CaFe3O5-type crystal structure that features linear chains of Fe ions. On cooling below ∼150 K, Fe4O5 undergoes an unusual charge-ordering transition that involves competing dimeric and trimeric ordering within the chains of Fe ions. This transition is concurrent with a significant increase in electrical resistivity. Magnetic-susceptibility measurements and neutron diffraction establish the formation of a collinear antiferromagnetic order above room temperature and a spin canting at 85 K that gives rise to spontaneous magnetization. We discuss possible mechanisms of this transition and compare it with the trimeronic charge ordering observed in magnetite below the Verwey transition temperature. PMID:27102685

Trimeric autotransporter adhesins (TAAs), cell surface proteins of Gram-negative bacteria, mediate bacterial adhesion to host cells and extracellular matrix proteins. However, AtaA, a TAA in the nonpathogenic Acinetobacter sp. strain Tol 5, shows nonspecific, high adhesiveness to abiotic material surfaces as well as to biotic surfaces. AtaA is a homotrimer of polypeptides comprising 3,630 amino acids and forms long nanofibers; therefore, it is too large and structurally complex to be produced as a recombinant protein. In this study, we isolated AtaA's passenger domain (AtaA PSD), which is translocated to the cell surface through the C-terminal transmembrane domain and exhibits biological functions, using a new method. We introduced a protease recognition site and reaped AtaA nanofibers 225 nm in length from the cell surface through proteolytic cleavage with a specific protease. Biochemical and biophysical analyses of the purified native AtaA PSD revealed that it has a stable structure under alkaline and acidic conditions. Temperatures above 80 °C, which disrupted AtaA's higher-order structure but maintained the full-length AtaA polypeptide, inactivated AtaA's nonspecific adhesiveness, suggesting that the stickiness of AtaA requires its 3D structure. This finding refutes the widespread but vague speculation that large unfolded polypeptides readily stick to various surfaces. PMID:27305955

Phase transitions that occur in materials, driven, for instance, by changes in temperature or pressure, can dramatically change the materials’ properties. Discovering new types of transitions and understanding their mechanisms is important not only from a fundamental perspective, but also for practical applications. Here we investigate a recently discovered Fe4O5 that adopts an orthorhombic CaFe3O5-type crystal structure that features linear chains of Fe ions. On cooling below ∼150 K, Fe4O5 undergoes an unusual charge-ordering transition that involves competing dimeric and trimeric ordering within the chains of Fe ions. This transition is concurrent with a significant increase in electrical resistivity. Magnetic-susceptibility measurements and neutron diffraction establish the formation of a collinear antiferromagnetic order above room temperature and a spin canting at 85 K that gives rise to spontaneous magnetization. We discuss possible mechanisms of this transition and compare it with the trimeronic charge ordering observed in magnetite below the Verwey transition temperature.

The membrane-proximal external region (MPER) of HIV-1 gp41 is an attractive target for vaccine development. Thus, better understanding of its immunogenic properties in various structural contexts is important. We previously described the crystal structure of a trimeric protein complex named gp41-HR1-54Q, which consists of the heptad repeat regions 1 and 2 and the MPER. The protein was efficiently recognized by broadly neutralizing antibodies. Here, we describe its immunogenic properties in rabbits. The protein was highly immunogenic, especially the C-terminal end of the MPER containing 4E10 and 10E8 epitopes ((671)NWFDITNWLWYIK(683)). Although antibodies exhibited strong competition activity against 4E10 and 10E8, neutralizing activity was not detected. Detailed mapping analyses indicated that amino acid residues critical for recognition resided on faces of the alpha helix that are either opposite of or perpendicular to the epitopes recognized by 4E10 and 10E8. These results provide critical information for designing the next generation of MPER-based immunogens. PMID:26454663

Trimeric autotransporter adhesins (TAAs), cell surface proteins of Gram-negative bacteria, mediate bacterial adhesion to host cells and extracellular matrix proteins. However, AtaA, a TAA in the nonpathogenic Acinetobacter sp. strain Tol 5, shows nonspecific, high adhesiveness to abiotic material surfaces as well as to biotic surfaces. AtaA is a homotrimer of polypeptides comprising 3,630 amino acids and forms long nanofibers; therefore, it is too large and structurally complex to be produced as a recombinant protein. In this study, we isolated AtaA’s passenger domain (AtaA PSD), which is translocated to the cell surface through the C-terminal transmembrane domain and exhibits biological functions, using a new method. We introduced a protease recognition site and reaped AtaA nanofibers 225 nm in length from the cell surface through proteolytic cleavage with a specific protease. Biochemical and biophysical analyses of the purified native AtaA PSD revealed that it has a stable structure under alkaline and acidic conditions. Temperatures above 80 °C, which disrupted AtaA’s higher-order structure but maintained the full-length AtaA polypeptide, inactivated AtaA’s nonspecific adhesiveness, suggesting that the stickiness of AtaA requires its 3D structure. This finding refutes the widespread but vague speculation that large unfolded polypeptides readily stick to various surfaces. PMID:27305955

Previously we described induction of cross-reactive HIV-1 neutralizing antibody responses in rabbits using a soluble HIV-1 gp140 envelope glycoprotein (Env) in an adjuvant containing monophosphoryl lipid A (MPL) and QS21 (AS02A). Here, we compared different forms of the same HIV-1 strain R2 Env for antigenic and biophysical characteristics, and in rabbits characterized the extent of B cell induction for specific antibody expression and secretion and neutralizing responses. The forms of this Env that were produced in and purified from stably transformed 293T cells included a primarily dimeric gp140, a trimeric gp140 appended to a GCN4 trimerization domain (gp140-GCN4), gp140-GCN4 with a 15 amino acid flexible linker between the gp120 and gp41 ectodomain (gp140-GCN4-L), also trimeric, and a gp140 with the flexible linker purified from cell culture supernatants as either dimer (gp140-L(D)) or monomer (gp140-L(M)). Multimeric states of the Env proteins were assessed by native gel electrophoresis and analytical ultracentrifugation. The different forms of gp140 bound broadly cross-reactive neutralizing (BCN) human monoclonal antibodies (mAbs) similarly in ELISA and immunoprecipitation assays. All Envs bound CD4i mAbs in the presence and absence of sCD4, as reported for the R2 Env. Weak neutralization of some strains of HIV-1 was seen after two additional doses in AS02A. Rabbits that were given a seventh dose of gp140-GCN4-L developed BCN responses that were weak to moderate, similar to our previous report. The specificity of these responses did not appear similar to that of any of the known BCN human mAbs. Induction of spleen B cell and plasma cells producing immunoglobulins that bound trimeric gp140-GCN4-L was vigorous, based on ELISpot and flow cytometry analyses. The results demonstrate that highly purified gp140-GCN4-L trimer in adjuvant elicits BCN responses in rabbits accompanied by vigorous B cell induction. PMID:24846288

Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs. We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. In some trimeric ESTs, the downstream partner was fused to the poly-A tail of the upstream partner, which, together with the mtRNA-nRNA fusions, suggests a possible new mechanism for RNA fusion that occurs after both transcription and splicing have been terminated, and possibly outside the nucleus, in contrast to the two current hypothetical mechanisms, trans-splicing and transcriptional-slippage, that occur in the nucleus. The mt-sequences in the mtRNA-nRNA fusions had pseudogenes in the nucleus but, surprisingly, localized mainly in chromosomes 1 and 5. In some mtRNA-nRNA fusions, as well as in some ESTs that were derived only from mtRNA, the mt-sequences might be cis- or trans-spliced. Actually, we cloned a new cis-spliced mtRNA, coined as 16SrRNA-s. Hence, mtDNA may not always be intron-less. Fusion of three or more RNAs to one, fusion of nRNA to mtRNA, and cis- or trans-splicing of mtRNA should all enlarge the cellular RNA repertoire, in turn enlarging the cellular functions. Therefore, future experimental verification of the existence of these novel classes of fusion RNAs and spliced mtRNAs in human cells should significantly advance our understanding of biology and medicine. PMID:24204722

Adenoviral vectored vaccines have shown considerable promise but could be improved by molecular adjuvants. Ligands in the TNF superfamily (TNFSF) are potential adjuvants for adenoviral vector (Ad5) vaccines based on their central role in adaptive immunity. Many TNFSF ligands require aggregation beyond the trimeric state (multi-trimerization) for optimal biological function. Here we describe Ad5 vaccines for HIV-1 Gag antigen (Ad5-Gag) adjuvanted with the TNFSF ligands 4-1BBL, BAFF, GITRL and CD27L constructed as soluble multi-trimeric proteins via fusion to Surfactant Protein D (SP-D) as a multimerization scaffold. Mice were vaccinated with Ad5-Gag combined with Ad5 expressing one of the SP-D-TNFSF constructs or single-chain IL-12p70 as adjuvant. To evaluate vaccine-induced protection, mice were challenged with vaccinia virus expressing Gag (vaccinia-Gag) which is known to target the female genital tract, a major route of sexually acquired HIV-1 infection. In this system, SP-D-4-1BBL or SP-D-BAFF led to significantly reduced vaccinia-Gag replication when compared to Ad5-Gag alone. In contrast, IL-12p70, SP-D-CD27L and SP-D-GITRL were not protective. Histological examination following vaccinia-Gag challenge showed a dramatic lymphocytic infiltration into the uterus and ovaries of SP-D-4-1BBL and SP-D-BAFF-treated animals. By day 5 post challenge, proinflammatory cytokines in the tissue were reduced, consistent with the enhanced control over viral replication. Splenocytes had no specific immune markers that correlated with protection induced by SP-D-4-1BBL and SP-D-BAFF versus other groups. IL-12p70, despite lack of anti-viral efficacy, increased the total numbers of splenic dextramer positive CD8+ T cells, effector memory T cells, and effector Gag-specific CD8+ T cells, suggesting that these markers are poor predictors of anti-viral immunity in this model. In conclusion, soluble multi-trimeric 4-1BBL and BAFF adjuvants led to strong protection from vaccinia

The crystal structure of the binary complex of trimeric purine nucleoside phosphorylase (PNP) from calf spleen with the acyclic nucleoside phosphonate inhibitor 2,6-diamino-(S)-9-[2-(phosphonomethoxy)propyl]purine ((S)-PMPDAP) is determined at 2.3A resolution in space group P2(1)2(1)2(1). Crystallization in this space group, which is observed for the first time with a calf spleen PNP crystal structure, is obtained in the presence of calcium atoms. In contrast to the previously described cubic space group P2(1)3, two independent trimers are observed in the asymmetric unit, hence possible differences between monomers forming the biologically active trimer could be detected, if present. Such differences would be expected due to third-of-the-sites binding documented for transition-state events and inhibitors. However, no differences are noted, and binding stoichiometry of three inhibitor molecules per enzyme trimer is observed in the crystal structure, and in the parallel solution studies using isothermal titration calorimetry and spectrofluorimetric titrations. Presence of phosphate was shown to modify binding stoichiometry of hypoxanthine. Therefore, the enzyme was also crystallized in space group P2(1)2(1)2(1) in the presence of (S)-PMPDAP and phosphate, and the resulting structure of the binary PNP/(S)-PMPDAP complex was refined at 2.05A resolution. No qualitative differences between complexes obtained with and without the presence of phosphate were detected, except for the hydrogen bond contact of Arg84 and a phosphonate group, which is observed only in the former complex in three out of six independent monomers. Possible hydrogen bonds observed in the enzyme complexed with (S)-PMPDAP, in particular a putative hydrogen bonding contact N(1)-H cdots, three dots, centered Glu201, indicate that the inhibitor binds in a tautomeric or ionic form in which position N(1) acts as a hydrogen bond donor. This points to a crucial role of this hydrogen bond in defining

Trimeric autotransporter adhesins (TAAs), fibrous proteins on the cell surface of Gram-negative bacteria, have attracted attention as virulence factors. However, little is known about the mechanism of their biogenesis. AtaA, a TAA of Acinetobacter sp. Tol 5, confers nonspecific, high adhesiveness to bacterial cells. We identified a new gene, tpgA, which forms a single operon with ataA and encodes a protein comprising two conserved protein domains identified by Pfam: an N-terminal SmpA/OmlA domain and a C-terminal OmpA_C-like domain with a peptidoglycan (PGN)-binding motif. Cell fractionation and a pull-down assay showed that TpgA forms a complex with AtaA, anchoring it to the outer membrane (OM). Isolation of total PGN-associated proteins showed TpgA binding to PGN. Disruption of tpgA significantly decreased the adhesiveness of Tol 5 because of a decrease in surface-displayed AtaA, suggesting TpgA involvement in AtaA secretion. This is reminiscent of SadB, which functions as a specific chaperone for SadA, a TAA in Salmonella species; however, SadB anchors to the inner membrane, whereas TpgA anchors to the OM through AtaA. The genetic organization encoding the TAA-TpgA-like protein cassette can be found in diverse Gram-negative bacteria, suggesting a common contribution of TpgA homologues to TAA biogenesis. PMID:27074146

The Scar/WAVE-complex links upstream Rho-GTPase signaling to the activation of the conserved Arp2/3-complex. Scar/WAVE-induced and Arp2/3-complex-mediated actin nucleation is crucial for actin assembly in protruding lamellipodia to drive cell migration. The heteropentameric Scar/WAVE-complex is composed of Scar/WAVE, Abi, Nap, Pir and a small polypeptide Brk1/HSPC300, and recent work suggested that free Brk1 serves as a homooligomeric precursor in the assembly of this complex. Here we characterized the Brk1 trimer from Dictyostelium by analytical ultracentrifugation and gelfiltration. We show for the first time its dissociation at concentrations in the nanomolar range as well as an exchange of subunits within different DdBrk1 containing complexes. Moreover, we determined the three-dimensional structure of DdBrk1 at 1.5 Å resolution by X-ray crystallography. Three chains of DdBrk1 are associated with each other forming a parallel triple coiled-coil bundle. Notably, this structure is highly similar to the heterotrimeric α-helical bundle of HSPC300/WAVE1/Abi2 within the human Scar/WAVE-complex. This finding, together with the fact that Brk1 is collectively sandwiched by the remaining subunits and also constitutes the main subunit connecting the triple-coil domain of the HSPC300/WAVE1/Abi2/ heterotrimer to Sra1(Pir1), implies a critical function of this subunit in the assembly process of the entire Scar/WAVE-complex. PMID:21701600

A long-standing issue in the field of signal transduction is to understand the cross-talk between receptor tyrosine kinases (RTKs) and heterotrimeric G proteins, two major and distinct signaling hubs that control eukaryotic cell behavior. Although stimulation of many RTKs leads to activation of trimeric G proteins, the molecular mechanisms behind this phenomenon remain elusive. We discovered a unifying mechanism that allows GIV/Girdin, a bona fide metastasis-related protein and a guanine-nucleotide exchange factor (GEF) for Gαi, to serve as a direct platform for multiple RTKs to activate Gαi proteins. Using a combination of homology modeling, protein–protein interaction, and kinase assays, we demonstrate that a stretch of ∼110 amino acids within GIV C-terminus displays structural plasticity that allows folding into a SH2-like domain in the presence of phosphotyrosine ligands. Using protein–protein interaction assays, we demonstrated that both SH2 and GEF domains of GIV are required for the formation of a ligand-activated ternary complex between GIV, Gαi, and growth factor receptors and for activation of Gαi after growth factor stimulation. Expression of a SH2-deficient GIV mutant (Arg 1745→Leu) that cannot bind RTKs impaired all previously demonstrated functions of GIV—Akt enhancement, actin remodeling, and cell migration. The mechanistic and structural insights gained here shed light on the long-standing questions surrounding RTK/G protein cross-talk, set a novel paradigm, and characterize a unique pharmacological target for uncoupling GIV-dependent signaling downstream of multiple oncogenic RTKs. PMID:25187647

Targeted radiopharmaceutical is an effective treatment for solid tumors. By labeling with radionuclides, targeting peptide could achieve both noninvasive diagnosis and targeted radionuclide therapy. In order to evaluate the potential applicability of GEBP11 peptides in diagnosis and radiotherapy of gastric cancer, in this study, iodine 131 labeled GEBP11 peptides, including a novel bifid PEGlylated GEBP11 trimer and its corresponding monomer, were developed. The clinical potential of GEBP11 peptides, such as tumor binding affinity and antitumor efficacy was demonstrated and assessed with multimodality imaging methods. Cerenkov and SPECT imaging showed higher tumor uptake for (131)I-2PEG-(GEBP11)3 (P<0.05, day 1; P<0.01, day 2; vs. monomer). Biodistribution studies indicated higher tumor accumulation and better T/NT of (131)I-2PEG-(GEBP11)3. Bioluminescence imaging exhibited a significant tumor growth suppression in (131)I-2PEG-(GEBP11)3 treated group (P<0.001 vs. control; P<0.01 vs. monomer). After treatment with (131)I-2PEG-(GEBP11)3, the tumor volume and vasculature decreased significantly, and the survival time was prolonged to 75.5days. Meanwhile, no significant hepatic or renal toxicity was observed with (131)I-2PEG-(GEBP11)3 administered. In conclusion, (131)I-2PEG-(GEBP11)3 could be a promising candidate for peptide-based targeting therapy of gastric cancer. 2PEG-(GEBP11)3 might be a potential drug delivery vehicle for the antiangiogenic therapy of gastric cancer. PMID:24012487

Background The life-cycle of cellular slime molds comprises chronobiologically regulated processes. During the growth phase, the amoeboid cells proliferate at a definite rate. Upon starvation, they synthesize cAMP as both first and second messengers in signalling pathways and form aggregates, migrating slugs, and fruiting bodies, consisting of spores and stalk cells, within 24 h. In Dictyostelium discoideum, because most growth-specific events cease during development, proliferative and heterochronic mutations are not considered to be interrelated and no genetic factor governing the entire life-cycle duration has ever been identified. Methodology/Principal Findings Using yeast 2-hybrid library screening, we isolated a Dictyostelium discoideum RabGAP, Dd Rbg-3, as a candidate molecule by which the Dictyostelium Gα2 subunit directs its effects. Rab GTPase-activating protein, RabGAP, acts as a negative regulator of Rab small GTPases, which orchestrate the intracellular membrane trafficking involved in cell proliferation. Deletion mutants of Dd rbg-3 exhibited an increased growth rate and a shortened developmental period, while an overexpression mutant demonstrated the opposite effects. We also show that Dd Rbg-3 interacts with 2 Gα subunits in an activity-dependent manner in vitro. Furthermore, both human and Caenorhabditis elegans rbg-3 homologs complemented the Dd rbg-3–deletion phenotype in D. discoideum, indicating that similar pathways may be generally conserved in multicellular organisms. Conclusions/Significance Our findings suggest that Dd Rbg-3 acts as a key element regulating the duration of D. discoideum life-span potentially via trimeric G-protein cascades. PMID:24349132

The solvothermal reaction of DyCl3·6H2O, Ni(NO3)2·6H2O, and H4abtc ligands (H4abtc = 3,3',5,5'-azobenzene-tetracarboxylic acid) in the mixed DMF/H2O solvents (DMF = N,N-dimethylformamide) produced a three-dimensional (3D) Ni(II)-Dy(III) heterometallic coordination polymer (HCP) formulated as {[NH2(CH3)2]2[NiDy2(HCOO)2(abtc)2]}n (1). In 1, Dy(III) and Ni(II) ions interconnect through carboxylic O donors of abtc(4-) ligands to generate a linear trimer "Hourglass"-type {NiDy2} cluster, and the adjacent trinuclear {NiDy2} units are bridged by HCOO(-) groups to give a 1D "ladder" chain, which is further bridged by abtc(4-) ligands to form a new topology and named as "zsw3". Alternating-current magnetic susceptibility results indicate that 1 exhibits frequency-dependent out-of-phase signals with two relaxation processes, which suggests that it shows single-molecule magnet (SMM) behavior and represents the first example by using an SMM cluster as the building block to create a 3D Ni-Ln HCP, to the best of our knowledge. The energy barriers for 1 under a 1000 Oe applied direct current magnetic field are estimated from Arrhenius plots to be 40 and 42 K at higher and lower frequencies, respectively. Additionally, the crystalline structure of 1 could be stable to at least 310 °C, supported by thermogravimetric analyses and in situ variable-temperature powder X-ray diffraction patterns. PMID:26751740

In gram-negative bacteria, the assembly of type IV pilus (T4P) and the evolutionally related pseudopilus of type II secretion system involves specialized structural proteins called pilins and pseudopilins, respectively, and is dynamically regulated to promote bacterial pathogenesis. Previous studies have suggested that a structural "tip"-like hetero-complex formed through the interaction of at least three minor (pseudo) pilins plays an important role in this process, while some members of the pathogenic type IVb subfamily are known to have only one such minor pilin subunit whose function is still unknown. Here, we determined the crystal structure of the type IVb minor pilin CofB of colonization factor antigen/III from human enterotoxigenic Escherichia coli at 1.88-Å resolution. The crystal structure, in conjunction with physicochemical analysis in solution, reveals a symmetrical homo-trimeric arrangement distinct from the hetero-complexes of minor (pseudo) pilins observed in other T4P and type II secretion systems. Each CofB monomer adopts a unique three-domain architecture, in which the C-terminal β-sheet-rich lectin domain can effectively initiate trimer association of its pilin-like N-terminal domain through extensive hydrophobic interactions followed by domain swapping at the central hinge-like domain. Deletion of cofB produces a phenotype with no detectable pili formation on the cell surface, while molecular modeling indicates that the characteristic homo-trimeric structure of CofB is well situated at the pilus tip of colonization factor antigen/III formed by the major pilin CofA, suggesting a role for the minor pilin in the efficient initiation of T4P assembly. PMID:26876601

Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution. All gp26-like factors contain an elongated {alpha}-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 {angstrom}. gp26 tail needles display a high level of structural stability in solution, with Tm (temperature of melting) between 85 and 95 C. To determine how the structural stability of these phage fibers correlates with the length of the {alpha}-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the {alpha}-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the {alpha}-helical core.

The amyloid-β protein (Aβ) oligomers are believed to be the main culprits in the cytoxicity of Alzheimer's disease (AD) and p3 peptides (Aβ17-42 fragments) are present in AD amyloid plaques. Many small-molecule or peptide-based inhibitors are known to slow down Aβ aggregation and reduce the toxicity in vitro, but their exact modes of action remain to be determined since there has been no atomic level of Aβ(p3)-drug oligomers. In this study, we have determined the structure of Aβ17-42 trimers both in aqueous solution and in the presence of five small-molecule inhibitors using a multiscale computational study. These inhibitors include 2002-H20, curcumin, EGCG, Nqtrp, and resveratrol. First, we used replica exchange molecular dynamics simulations coupled to the coarse-grained (CG) OPEP force field. These CG simulations reveal that the conformational ensemble of Aβ17-42 trimer can be described by 14 clusters with each peptide essentially adopting turn/random coil configurations, although the most populated cluster is characterized by one peptide with a β-hairpin at Phe19-Leu31. Second, these 14 dominant clusters and the less-frequent fibril-like state with parallel register of the peptides were subjected to atomistic Autodock simulations. Our analysis reveals that the drugs have multiple binding modes with different binding affinities for trimeric Aβ17-42 although they interact preferentially with the CHC region (residues 17-21). The compounds 2002-H20 and Nqtrp are found to be the worst and best binders, respectively, suggesting that the drugs may interfere at different stages of Aβ oligomerization. Finally, explicit solvent molecular dynamics of two predicted Nqtrp-Aβ17-42 conformations describe at atomic level some possible modes of action for Nqtrp. PMID:22283547

We previously identified Treponema pallidum repeat proteins TprC/D, TprF, and TprI as candidate outer membrane proteins (OMPs) and subsequently demonstrated that TprC is not only a rare OMP but also forms trimers and has porin activity. We also reported that TprC contains N- and C-terminal domains (TprC(N) and TprC(C)) orthologous to regions in the major outer sheath protein (MOSP(N) and MOSP(C)) of Treponema denticola and that TprC(C) is solely responsible for β-barrel formation, trimerization, and porin function by the full-length protein. Herein, we show that TprI also possesses bipartite architecture, trimeric structure, and porin function and that the MOSP(C)-like domains of native TprC and TprI are surface-exposed in T. pallidum, whereas their MOSP(N)-like domains are tethered within the periplasm. TprF, which does not contain a MOSP(C)-like domain, lacks amphiphilicity and porin activity, adopts an extended inflexible structure, and, in T. pallidum, is tightly bound to the protoplasmic cylinder. By thermal denaturation, the MOSP(N) and MOSP(C)-like domains of TprC and TprI are highly thermostable, endowing the full-length proteins with impressive conformational stability. When expressed in Escherichia coli with PelB signal sequences, TprC and TprI localize to the outer membrane, adopting bipartite topologies, whereas TprF is periplasmic. We propose that the MOSP(N)-like domains enhance the structural integrity of the cell envelope by anchoring the β-barrels within the periplasm. In addition to being bona fide T. pallidum rare outer membrane proteins, TprC/D and TprI represent a new class of dual function, bipartite bacterial OMP. PMID:25805501

The mature human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer is produced by proteolytic cleavage of a precursor and consists of three gp120 exterior and three gp41 transmembrane subunits. The metastable Env complex is induced to undergo conformational changes required for virus entry by the binding of gp120 to the receptors, CD4 and CCR5/CXCR4. An isoleucine-to-proline change (I559P) in the gp41 ectodomain has been used to stabilize soluble forms of HIV-1 Env trimers for structural characterization and for use as immunogens. In the native membrane-anchored HIV-1BG505 Env, the I559P change modestly decreased proteolytic maturation, increased the non-covalent association of gp120 with the Env trimer, and resulted in an Env conformation distinctly different from that of the wild-type HIV-1BG505 Env. Compared with the wild-type Env, the I559P Env was recognized inefficiently by polyclonal sera from HIV-1-infected individuals, by several gp41-directed antibodies, by some antibodies against the CD4-binding site of gp120, and by antibodies that preferentially recognize the CD4-bound Env. Some of the gp120-associated antigenic differences between the wild-type HIV-1BG505 Env and the I559P mutant were compensated by the SOS disulfide bond between gp120 and gp41, which has been used to stabilize cleaved soluble Env trimers. Nonetheless, regardless of the presence of the SOS changes, Envs with proline 559 were recognized less efficiently than Envs with isoleucine 559 by the VRC01 neutralizing antibody, which binds the CD4-binding site of gp120, and the PGT151 neutralizing antibody, which binds a hybrid gp120-gp41 epitope. The I559P change completely eliminated the ability of the HIV-1BG505 Env to mediate cell-cell fusion and virus entry, and abolished the capacity of the SOS Env to support virus infection in the presence of a reducing agent. These results suggest that differences exist between the quaternary structures of functional Env spikes and I559P

Using B3LYP and B97D functionals of density functional theory (DFT), homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids are studied in gas phase and solvent phase, i. e., Acetonitrile. Both the functionals show that formation of homochiral cyclic tripeptide is thermodynamically and kinetically favorable over its heterochiral counterpart in gas phase. The functional, B97D, decreases the height of reaction barriers significantly compared to those predicted by the functional B3LYP. The reaction pathways explored using PCM implicit solvent model show reduced kinetic favorability for formation of the homochiral cyclic tripeptide over its heterochiral counterpart. The results are substantiated by structural aspects. PMID:27221744

The opportunistic pathogen Pseudomonas aeruginosa ranks among leading causes of nosocomial infections. The type III secretion system (T3SS) aids acute P. aeruginosa infections by injecting potent cytotoxins into host cells to suppress the host's innate immune response. Expression of all T3SS-related genes is strictly dependent upon the transcription factor ExsA. Consequently, ExsA and the biological processes that regulate ExsA function are of great biomedical interest. The presented work focuses on the ExsA-ExsC-ExsD-ExsE signaling cascade that ties host cell contact to the up-regulation of T3SS gene expression. Prior to T3SS induction, the anti-activator protein ExsD binds to ExsA and blocks ExsA-dependent transcription by interfering with ExsA dimerization and promoter interactions. Upon host cell contact, ExsD is sequestered by the T3SS chaperone ExsC resulting in the release of ExsA and an up-regulation of the T3SS. Previous studies have shown that the ExsD-ExsA interactions are not freely reversible. Because independently folded ExsD and ExsA were not found to interact, it has been hypothesized that folding intermediates of the two proteins form the complex. Here we demonstrate for the first time that ExsD alone is sufficient to inhibit ExsA-dependent transcription in vitro and that no other cellular factors are required. More significantly, we show that independently folded ExsD and ExsA are capable of interacting, but only at 37°C and not at 30°C. Guided by the crystal structure of ExsD, we designed a monomeric variant of the protein and demonstrate that ExsD trimerization prevents ExsD from inhibiting ExsA-dependent transcription at 30°C. We propose that this unique mechanism plays an important role in T3SS regulation. PMID:23279839

A computational study of model halogen-bonded FCl … YZ dimers and FX‧ … FCl … YZ (FX‧ = FH, FCl, F2Be; YZ = BF, CO, N2) trimers was undertaken at the MP2/6-311++G (2d, 2p) level of theory. Three different trimer arrangements are possible and the cooperative effect of hydrogen-, halogen- and beryllium-bonding in each of these trimers was assessed relative to the FCl … YZ dimer. It was found that the beryllium bond has the largest cooperative effect, while the halogen bond has the smallest, with the hydrogen bond being intermediate between the other two interactions. Interesting trends in selected properties were identified and discussed.

The reaction mechanisms of silver trimer cation, Ag{sub 3}{sup +}, with 12-crown-4 (12C4) were studied experimentally and theoretically. Using a cylindrical ion trap time-of-flight mass spectrometer, gas-phase ion/molecule reactions of Ag{sub 3}{sup +} with 12C4 were observed. Metal-ligand complexes of [Ag(12C4)]{sup +}, [Ag{sub 3}(12C4)]{sup +} and [Ag{sub 3}(12C4){sub 2}]{sup +}, and of [Ag(12C4){sub 2}]{sup +} and [Ag{sub 3}(12C4){sub 3}]{sup +}, were observed as the reaction intermediates and terminal products, respectively. The formations of the [Ag(12C4)]{sup +} and [Ag(12C4){sub 2}]{sup +} complexes indicated that the neutral dimer (Ag{sub 2}) had been eliminated from the trimer cation. From the results of ab initio calculations at the HF/LanL2DZ level of theory and the experiments, it is suggested that three 12C4 molecules can attach to Ag{sub 3}{sup +} through consecutive reactions and that neutral Ag{sub 2} can be easily eliminated from [Ag{sub 3}(12C4)]{sup +}.

The [Au(CN)2−]3 trimer in water experiences a strong van der Waals interaction between the d10 gold atoms due to large relativistic effect and can serve as an excellent model system to study the bond formation process in real time. The trimer in the ground state (S0) exists as a bent structure without the covalent bond between the gold atoms, and upon the laser excitation, one electron in the antibonding orbital goes to the bonding orbital, thereby inducing the formation of a covalent bond between gold atoms. This process has been studied by various time-resolved techniques, and most of the interpretation on the structure and dynamics converge except that the structure of the first intermediate (S1) has been debated due to different interpretations between femtosecond optical spectroscopy and femtosecond X-ray solution scattering. Recently, the excitation wavelength of 267 nm employed in our previous scattering experiment was suggested as the culprit for misinterpretation. Here, we revisited this issue by performing femtosecond X-ray solution scattering with 310 nm excitation and compared the results with our previous study employing 267 nm excitation. The data show that a linear S1 structure is formed within 500 fs regardless of excitation wavelength and the structural dynamics observed at both excitation wavelengths are identical to each other within experimental errors. PMID:27191012

The ability to form and control both secondary structure and oligomerization in short peptides has proven to be challenging owing to the structural instability of such peptides. The conantokin peptides are a family of {gamma}-carboxyglutamic acid containing peptides produced in the venoms of predatory sea snails of the Conus family. They are examples of short peptides that form stable helical structures, especially in the presence of divalent cations. Both monomeric and dimeric conantokin peptides have been identified and represent a new mechanism of helix association, 'the metallozipper motif' that is devoid of a hydrophobic interface between monomers. In the present study, a parallel/antiparallel three-helix bundle was identified and its crystal structure determined at high resolution. The three helices are almost perfectly parallel and represent a novel helix-helix association. The trimer interface is dominated by metal chelation between the three helices, and contains no interfacial hydrophobic interactions. It is now possible to produce stable monomeric, dimeric, or trimeric metallozippers depending on the peptide sequence and metal ion. Such structures have important applications in protein design.

Temperature dependence in electronic energy transfer steps within light-harvesting antenna trimers from photosystem II was investigated by studying Chl a pump-probe anisotropy decays at several wavelengths from 675 to 682 nm. The anisotropy lifetime is markedly sensitive to temperature at the longest wavelengths (680-682 nm), increasing by factors of 5 to 6 as the trimers are cooled from room temperature to 13 K. The temperature dependence is muted at 677 and 675 nm. This behavior is modeled using simulations of temperature-broadened Chl a absorption and fluorescence spectra in spectral overlap calculations of Förster energy transfer rates. In this model, the 680 nm anisotropy decays are dominated by uphill energy transfers from 680 nm Chl a pigments at the red edge of the LHC-II spectrum; the 675 nm anisotropy decays reflect a statistical average of uphill and downhill energy transfers from 676-nm pigments. The measured temperature dependence is consistent with essentially uncorrelated inhomogeneous broadening of donor and acceptor Chl a pigments. PMID:8061208

The [Au(CN)2 (-)]3 trimer in water experiences a strong van der Waals interaction between the d(10) gold atoms due to large relativistic effect and can serve as an excellent model system to study the bond formation process in real time. The trimer in the ground state (S0) exists as a bent structure without the covalent bond between the gold atoms, and upon the laser excitation, one electron in the antibonding orbital goes to the bonding orbital, thereby inducing the formation of a covalent bond between gold atoms. This process has been studied by various time-resolved techniques, and most of the interpretation on the structure and dynamics converge except that the structure of the first intermediate (S1) has been debated due to different interpretations between femtosecond optical spectroscopy and femtosecond X-ray solution scattering. Recently, the excitation wavelength of 267 nm employed in our previous scattering experiment was suggested as the culprit for misinterpretation. Here, we revisited this issue by performing femtosecond X-ray solution scattering with 310 nm excitation and compared the results with our previous study employing 267 nm excitation. The data show that a linear S1 structure is formed within 500 fs regardless of excitation wavelength and the structural dynamics observed at both excitation wavelengths are identical to each other within experimental errors. PMID:27191012

We report a structural-magnetic investigation by x-ray absorption spectroscopy (XAS), neutron diffraction, dc susceptibility (χdc), and electron spin resonance (ESR) of the 12R-type perovskite BaTi1/2Mn1/2O3 . Our structural analysis by neutron diffraction supports the existence of structural trimers with chemically disordered occupancy of Mn4+ and Ti4+ ions, with the valence of the Mn ions confirmed by the XAS measurements. The magnetic properties are explored by combining dc-susceptibility and X -band (9.4 GHz) electron spin resonance, both in the temperature interval of 2 ≤T ≤1000 K. A scenario is presented under which the magnetism is explained by considering magnetic dimers and trimers, with exchange constants Ja/kB=200 (2 ) K and Jb/kB=130 (10 ) K, and orphan spins. Thus, BaTi1/2Mn1/2O3 is proposed as a rare case of an intrinsically disordered S =3/2 spin gap system with a frustrated ground state.

We have recently proposed that the trimeric staphylococcal phage encoded dUTPases (Duts) are signaling molecules that act analogously to eukaryotic G-proteins, using dUTP as a second messenger. To perform this regulatory role, the Duts require their characteristic extra motif VI, present in all the staphylococcal phage coded trimeric Duts, as well as the strongly conserved Dut motif V. Recently, however, an alternative model involving Duts in the transfer of the staphylococcal islands (SaPIs) has been suggested, questioning the implication of motifs V and VI. Here, using state-of the-art techniques, we have revisited the proposed models. Our results confirm that the mechanism by which the Duts derepress the SaPI cycle depends on dUTP and involves both motifs V and VI, as we have previously proposed. Surprisingly, the conserved Dut motif IV is also implicated in SaPI derepression. However, and in agreement with the proposed alternative model, the dUTP inhibits rather than inducing the process, as we had initially proposed. In summary, our results clarify, validate and establish the mechanism by which the Duts perform regulatory functions. PMID:27112567

Triazine compounds and cross-linked polymer compositions are made by heating aromatic nitriles to a temperature in the range of from about 100 C to about 700 C, and preferably in the range of from about 200 C to about 350 C, in the presence of a catalyst or mixture of catalysts selected from one or more of the following groups: (1) organic sulfonic and sulfinic acids, (2) organic phosphonic and phosphinic acids, and (3)metallic acetylacetonates, at a pressure in the range of from about atmospheric pressure to about 10,000 psi and preferably in the range of from about 200 psi to about 750 psi. Aromatic nitrile-modified (terminated and/or appended) imide, benzimidazole, imidazopyrrolone, quinoxaline, and other condensation type prepolymers or their precopolymers are made which are trimerized with or without a filler by the aforementioned catalytic trimerization process into triaryl-s-triazine ring containing or cross-linked polymeric or copolymeric products useful in applications requiring high thermal-oxidative stability and high performance structural properties at elevated temperatures.

The synthesis and crystallographic characterization of a new family of M(mu-CN)Ln complexes are reported. Two structural series have been prepared by reacting in water rare earth nitrates (Ln(III) = La, Pr, Nd, Sm, Eu, Gd, Dy, Ho) with K(3)[M(CN)(6)] (M(III) = Fe, Co) in the presence of hexamethylenetetramine (hmt). The first series consists of six isomorphous heterobinuclear complexes, [(CN)(5)M-CN-Ln(H(2)O)(8)].2hmt ([FeLa] 1, [FePr] 2, [FeNd] 3, [FeSm] 4, [FeEu] 5, [FeGd] 6), while the second series consists of four isostructural ionic complexes, [M(CN)(6)][Ln(H(2)O)(8)].hmt ([FeDy] 7, [FeHo] 8, [CoEu] 9, [CoGd] 10). The hexamethylenetetramine molecules contribute to the stabilization of the crystals by participating in an extended network of hydrogen bond interactions. In both series the aqua ligands are hydrogen bonded to the nitrogen atoms from both the terminal CN(-) groups and the hmt molecules. The [FeGd] complex has been analyzed with (57)Fe Mossbauer spectroscopy and magnetic susceptibility measurements. We have also analyzed the [FeLa] complex, in which the paramagnetic Gd(III) is replaced by diamagnetic La(III), with (57)Fe Mossbauer spectroscopy, electron paramagnetic resonance (EPR), and magnetic susceptibility measurements, to obtain information about the low-spin Fe(III) site that is not accessible in the presence of a paramagnetic ion at the complementary site. For the same reason, the [CoGd] complex, containing diamagnetic Co(III), was studied with EPR and magnetic susceptibility measurements, which confirmed the S = 7/2 spin of Gd(III). Prior knowledge about the paramagnetic sites in [FeGd] allows a detailed analysis of the exchange interactions between them. In particular, the question of whether the exchange interaction in [FeGd] is isotropic or anisotropic has been addressed. Standard variable-temperature magnetic susceptibility measurements provide only the value for a linear combination of J(x), J(y), and J(z) but contain no information about the values of the individual exchange parameters J(x), J(y), and J(z). In contrast, the spin-Hamiltonian analysis of the variable-field, variable-temperature Mossbauer spectra reveals an exquisite sensitivity on the anisotropic exchange parameters. Analysis of these dependencies in conjunction with adopting the g-values obtained for [FeLa], yielded the values J(x) = +0.11 cm(-1), J(y) = +0.33 cm(-1), and J(z) = +1.20 cm(-1) (S(1).J.S(2) convention). The consistency of these results with magnetic susceptibility data is analyzed. The exchange anisotropy is rooted in the spatial anisotropy of the low-spin Fe(III) ion. The condition for anisotropic exchange is the presence of low-lying orbital excited states at the ferric site that (i) effectively interact through spin-orbit coupling with the orbital ground state and (ii) have an exchange parameter with the Gd site with a value different from that for the ground state. Density functional theory (DFT) calculations, without spin-orbit coupling, reveal that the unpaired electron of the t(2g)(5) ground configuration of the Fe(III) ion occupies the xy orbital, that is, the orbital along the plane perpendicular to the Fe...Gd vector. The exchange-coupling constants for this orbital, j(xy), and for the other t(2g) orbitals, j(yz) and j(xz), have been determined using a theoretical model that relates them to the anisotropic exchange parameters and the g-values of Fe(III). The resulting values, j(yz) = -5.7 cm(-1), j(xz) = -4.9 cm(-1), and j(xy) = +0.3 cm(-1) are quite different. The origin of the difference is briefly discussed. PMID:20225831

Recently we described roles for heterotrimeric and low-molecular-mass GTP-binding proteins in insulin release from normal rat islets. During these studies, we observed that a protein with an apparent molecular mass (37 kDa) similar to that of the beta subunit of trimeric GTP-binding proteins underwent phosphorylation in each of five classes of insulin-secreting cells. Incubation of the beta cell total membrane fraction or the isolated secretory granule fraction (but not the cytosolic fraction) with [gamma-32P]ATP or [gamma-32P]GTP resulted in the phosphorylation of this protein, which was selectively immunoprecipitated by an anti-serum directed against the common beta subunit of trimeric G-proteins. Disruption of the alpha beta gamma trimer (by pretreatment with either fluoroaluminate or guanosine 5'(-)[gamma-thio]triphosphate) prevented beta subunit phosphorylation. Based on differential sensitivities to pH, heat and the histidine-selective reagent diethyl pyrocarbonate (and reversal of the latter by hydroxylamine), the phosphorylated amino acid was presumptively identified as histidine. Incubation of pure beta subunit alone or in combination with the exogenous purified alpha subunit of transducin did not result in the phosphorylation of the beta subunit, but addition of the islet cell membrane fraction did support this event, suggesting that membrane localization (or a membrane-associated factor) is required for beta subunit phosphorylation. Incubation of phosphorylated beta subunit with G alpha.GDP accelerated the dephosphorylation of the beta subunit, accompanied by the formation of G alpha-GTP. Immunoblotting detected multiple alpha subunits (of Gi, G(o) and Gq) and at least one beta subunit in the secretory granule fraction of normal rat islets and insulinoma cells. These data describe a potential alternative mechanism for the activation of GTP-binding proteins in beta cells which contrasts with the classical receptor-agonist mechanism: G beta undergoes

Microwave spectra are reported for the C3v symmetric complexes Kr-SO3 and Kr-SO3-CO. The S-C distance in the trimer, 2.871(9) Å, is the same as that previously determined for SO3-CO to within the estimated uncertainties. The Kr-S distances are 3.438(3) Å and 3.488(6) Å in Kr-SO3 and Kr-SO3-CO, respectively, indicating that the addition of CO to Kr-SO3 increases the Kr-S distance by 0.050(9) Å. Measurements of the (83)Kr nuclear quadrupole coupling constants provide direct probes of the electric field gradient at the Kr nucleus, and a comparison between the two systems reflects the degree to which the CO influences the electronic structure of the krypton atom. Although the Kr and CO in the trimer are on opposite sides of the SO3 and thus are not in direct contact, the addition of CO to Kr-SO3 reduces the electric field gradient at the Kr nucleus by 18%. Calculations using the block localized wavefunction decomposition method are performed to understand the physical origins of this change. While the magnitudes of both the electric field and the electric field gradient at the Kr nucleus decrease upon addition of the CO to Kr-SO3, the changes are shown to arise from rather complex combinations of geometrical distortion, electrostatic, polarization, and electron transfer effects. For the electric field, the electrostatic term accounts for the largest portion of the reduction, while for the electric field gradient, polarization and structural change of the Kr-SO3 moiety make the primary contributions. Despite significant changes in the electronic environment at the Kr nucleus, calculated binding energies indicate that the interactions are largely additive, with the binding energy of the trimer very nearly equal to the sum of the Kr-SO3 and SO3-CO binding energies. PMID:23883040

We describe an efficient five-step, enantioselective synthesis of (R,R)- and (S,S)-lignin dimer models possessing a β-O-4 linkage, by using the Evans chiral aldol reaction as a key step. Mitsunobu inversion of the (R,R)- or (S,S)-isomers generates the corresponding (R,S)- and (S,R)-diastereomers. We further extend this approach to the enantioselective synthesis of a lignin trimer model. These lignin models are synthesized with excellent ee (>99 %) and high overall yields. The lignin dimer models can be scaled up to provide multigram quantities that are not attainable by using previous methodologies. These lignin models will be useful in degradation studies probing the selectivity of enzymatic, microbial, and chemical processes that deconstruct lignin. PMID:27459234

Motivated by recent experiments on volborthite single crystals showing a wide 1/3 -magnetization plateau, we perform microscopic modeling by means of density functional theory (DFT) with the single-crystal structural data as a starting point. Using DFT +U , we find four leading magnetic exchanges: antiferromagnetic J and J2, as well as ferromagnetic J' and J1. Simulations of the derived spin Hamiltonian show good agreement with the experimental low-field magnetic susceptibility and high-field magnetization data. The 1/3 -plateau phase pertains to polarized magnetic trimers formed by strong J bonds. An effective J →∞ model shows a tendency towards condensation of magnon bound states preceding the plateau phase.

The poor immunogenicity of many tumors can be partly explained by the inefficiency of the MHC class I peptide presentation pathway. MHC-I-based single-chain trimers (SCT) represent a new class of molecules with the potential to overcome this limitation. We here evaluated the ability of SCT presenting a melanoma antigen peptide (TRP-2) to prime cytotoxic T lymphocyte (CTL) responses in mice when given as DNA vaccines via Gene Gun or when expressed by dendritic cells. The SCT was unable to induce detectable priming or significant anti-tumor activity of CTL using either vaccination strategy, whereas control SCT (with an exogenous peptide) primed strong responses. This study thus provides the first data related to the use of SCT in combination with DC and their application toward self antigens and suggest this potent technology, alone, is insufficient to overcome self tolerance. PMID:20199770

The F(δ-)···F(δ-) intermolecular synthon was recently observed to be useful for generating a two-dimensional layered supramolecular architecture on the Ag(111) surface (Kawai, et al., ACS Nano, 2015). This was formed when the entirely negative covalently bonded fluorine atoms in phenyleneethynylene(bis(2,3,5,6-tetrafluoro-4-(2,3,4,5,6-pentafluorophenylethynyl)phenyl)-ethyne (BPEPE-F18)) were in close proximity to the same atoms in another BPEPE-F18 molecule. With a view to provide rigorous insights into the physical chemistry of such an intermolecular synthon, we have selected perfluorobenzene (C6F6) as a model compound, and have performed extensive DFT-M06-2X/6-311++G(d,p) investigations on a number of its homomolecular dimers, trimers, and tetramers. Of the twelve (C6F6)2 dimers investigated, a displaced-parallel arrangement with an uncorrected binding energy (ΔE) of -7.4 kcal mol(-1) was found to be the most stable, and an incorporation of the basis set superposition error (BSSE) has significantly reduced its ΔE to -4.7 kcal mol(-1). Besides, the ΔE for a minimum-energy least stable conformation of the same dimer, which involves a single σhole(-)···σhole(-) type F(δ-)···F(δ-) intermolecular bonding interaction, amounts to -0.62 and -0.24 kcal mol(-1) without and with BSSE, respectively. The geometry of another conformation of the dimer, which accompanies a set of three F(δ-)···F(δ-) intermolecular interactions somehow similarly to those observed in the layered supramolecular structure formed by the BPEPE-F18 molecules, lies at a relative energy of 6.5 kcal mol(-1) above the most stable conformation. Passing from the latter dimer to an analogous (C6F6)3 trimer, as well as from the trimer to an analogous (C6F6)4 tetramer, the latter two clusters comprising windmill-type F(δ-)···F(δ-) intermolecular topologies, we have marked a preferential increase in the value of ΔE from -0.94 (dimer) to -2.76 (trimer) to -4.49 kcal mol(-1) (tetramer

SUMMARY Broadly neutralizing antibodies to HIV are much sought-after (a) to guide vaccine design, both as templates and to inform on the authenticity of vaccine candidates, (b) to assist in structural studies and (c) as potential therapeutics. However, the number of targets on the viral envelope spike for such antibodies is limited. Here, we describe a set of human monoclonal antibodies that define a previously undefined target on HIV Env. The antibodies recognize a glycan-dependent epitope on the prefusion conformation of gp41 and unambiguously distinguish cleaved from uncleaved Env trimers, an important property given increasing evidence that cleavage is required for vaccine candidates that seek to mimic the functional HIV envelope spike. The availability of this set of antibodies expands the number of vaccine targets on HIV and provides reagents to characterize the native envelope spike. PMID:24768347

The formation of the mixed-stack donor-acceptor complex of dithieno [3,2-b:2‧,3‧-d]thiophene (1) and trimeric perfluoro-ortho-phenylene mercury (I) has been investigated under different conditions. Two solvatomorphs - mixed-stack complexes with a 1:1 donor-acceptor ratio and different solvent molecules in the solid state (dichloromethane (2) and dichloroethane (3)) have been obtained and characterized by experimental methods (FT-IR spectroscopy, differential thermogravimetric analysis, and X-ray crystallography) and quantum-chemical calculations at the density functional theory level. The differences in the solid state packing, thermal stability and potential charge-transfer properties of 2 and 3 are discussed.

Motivated by recent experiments on volborthite single crystals showing a wide 1/3-magnetization plateau, we perform microscopic modeling by means of density functional theory (DFT) with the single-crystal structural data as a starting point. Using DFT+U, we find four leading magnetic exchanges: antiferromagnetic J and J_{2}, as well as ferromagnetic J^{'} and J_{1}. Simulations of the derived spin Hamiltonian show good agreement with the experimental low-field magnetic susceptibility and high-field magnetization data. The 1/3-plateau phase pertains to polarized magnetic trimers formed by strong J bonds. An effective J→∞ model shows a tendency towards condensation of magnon bound states preceding the plateau phase. PMID:27472136

Infrared spectra of the CO2sbnd CO dimer are observed in the carbon monoxide CO stretch region (≈2150 cm-1). Combination bands yield the first experimental determinations of intermolecular mode frequencies for the planar T-shaped C-bonded form ('isomer 1'): 24.34 cm-1 for the in-plane CO rock and 43.96 cm-1 for the out-of-plane CO rock. These values are significantly higher than the analogous modes of the O-bonded form ('isomer 2'), previously determined to be 14.19 and 22.68 cm-1, respectively. New results are also reported for both isomers of the 12C18O2-substituted form of the dimer. Weak 'satellite bands' observed for both isomers are tentatively assigned to the trimer Hesbnd CO2sbnd CO.

The infrared spectrum of the water trimer trapped in solid neon has been identified. Eighteen groups of absorptions between 1600 and 11,000 cm -1 were assigned to one-, two- and three-quanta transitions of the intramolecular modes. Because of the near equivalence of the three molecules and their weak interactions most of these modes correspond to quasi degenerate vibrations involving the bending δ, free OH stretching (OH f) and bonded OH stretching (OH b) of the three subunits at 1608, 3725 and 3525-3473 cm -1, respectively. In the last case the 52 cm -1 splitting is due to the coupling between the OH b oscillators. Calculated anharmonic frequencies correctly agree with these observations and allow to propose a new assignment of the intermolecular modes. Finally combinations of intra + intermolecular transitions were identified and assigned on the basis of calculated anharmonicity coefficients.

Identification of Treponema pallidum rare outer membrane proteins (OMPs) has been a longstanding objective of syphilis researchers. We recently developed a consensus computational framework that employs a battery of cellular localization and topological prediction tools to generate ranked clusters of candidate rare OMPs (D. L. Cox et al., Infect. Immun. 78:5178–5194, 2010). TP0117/TP0131 (TprC/D), a member of the T. pallidum repeat (Tpr) family, was a highly ranked candidate. Circular dichroism, heat modifiability by SDS-PAGE, Triton X-114 phase partitioning, and liposome incorporation confirmed that full-length, recombinant TprC (TprCFl) forms a β-barrel capable of integrating into lipid bilayers. Moreover, TprCFl increased efflux of terbium-dipicolinic acid complex from large unilamellar vesicles and migrated as a trimer by blue-native PAGE. We found that in T. pallidum, TprC is heat modifiable, trimeric, expressed in low abundance, and, based on proteinase K accessibility and opsonophagocytosis assays, surface exposed. From these collective data, we conclude that TprC is a bona fide rare OMP as well as a functional ortholog of Escherichia coli OmpF. We also discovered that TprC has a bipartite architecture consisting of a soluble N-terminal portion (TprCN), presumably periplasmic and bound directly or indirectly to peptidoglycan, and a C-terminal β-barrel (TprCC). Syphilitic rabbits generate antibodies exclusively against TprCC, while secondary syphilis patients fail to mount a detectable antibody response against either domain. The syphilis spirochete appears to have resolved a fundamental dilemma arising from its extracellular lifestyle, namely, how to enhance OM permeability without increasing its vulnerability to the antibody-mediated defenses of its natural human host. PMID:22389487

Though vaccination with live-attenuated SIV provides the greatest protection from progressive disease caused by SIV challenge in rhesus macaques, attenuated HIV presents safety concerns as a vaccine; therefore, live viral vectors carrying HIV immunogens must be considered. We have designed a replication-competent vesicular stomatitis virus (VSV) displaying immunogenic HIV-1 Env trimers and attenuating quantities of the native surface glycoprotein (G). The clade B Env immunogen is an Env-VSV G hybrid (EnvG) in which the transmembrane and cytoplasmic tail regions are derived from G. Relocation of the G gene to the 5′terminus of the genome and insertion of EnvG into the natural G position induced a ∼1 log reduction in surface G, significant growth attenuation compared to wild-type, and incorporation of abundant EnvG. Western blot analysis indicated that ∼75% of incorporated EnvG was a mature proteolytically processed form. Flow cytometry showed that surface EnvG bound various conformationally- and trimer-specific antibodies (Abs), and in-vitro growth assays on CD4+CCR5+ cells demonstrated EnvG functionality. Neither intranasal (IN) or intramuscular (IM) administration in mice induced any observable pathology and all regimens tested generated potent Env-specific ELISA titers of 104–105, with an IM VSV prime/IN VSV boost regimen eliciting the highest binding and neutralizing Ab titers. Significant quantities of Env-specific CD4+ T cells were also detected, which were augmented as much as 70-fold by priming with IM electroporated plasmids encoding EnvG and IL-12. These data suggest that our novel vector can achieve balanced safety and immunogenicity and should be considered as an HIV vaccine platform. PMID:25215861

The complex [gamma(1,2)-SiW(10){Fe(OH(2))}(2)O(38)](6)(-) (1) has been reported to catalyze the much sought reductant-free selective O(2)-based epoxidation of alkenes (Nishiyama, Y.; Nakagawa, Y.; Mizuno, N. Angew. Chem. Int. Ed. 2001, 40, 3639-3641) in chlorocarbon-acetonitrile solution. The challenge of reproducing catalysis by 1 led us to examine this chemistry in detail. In H(2)O, a desirable solvent for catalysis, 1, does not exist in the proposed organic-medium form in which the two iron atoms are in the binding pocket defined by the equatorial oxygens and, importantly, by two oxygens bound to the central Si heteroatom. Instead, 1 in H(2)O initially forms an unusual trimer [{Fe(2)(OH)(3)(H(2)O)(2)}(3)(gamma-SiW(10)O(36))(3)](15)(-) (2). The X-ray structure of 2 shows that the Fe-O(Si) bonds are cleaved and new bonds (mu-hydroxo bridges) form between these Fe centers and those of the neighboring [gamma(1,2)-SiW(10)Fe(2)] units. Structural, physical, and computational evidence indicate that if the bonds between the d-electron center, M (Fe in the case of 1 and 2), and the terminal ligands on M are stronger than the M-O(x)() bonds, then the out-of-pocket form is more stable and is the one observed. Significantly, 2 in H(2)O forms an intermediate that catalyzes the effective aerobic oxidation of sulfur compounds (mercaptoethanol is oxidized to the corresponding disulfide by O(2) at ambient pressure and temperature). All experimental findings are consistent with dissociation of a gamma-SiW(10) Keggin unit from the trimer, 2, to form the catalytically active species. PMID:16925446

The HIV-1 envelope gp160 glycoprotein (Env) is a trimer of gp120 and gp41 heterodimers that mediates cell entry and is the primary target of the humoral immune response. Broadly neutralizing antibodies (bNAbs) to HIV-1 have revealed multiple epitopes or sites of vulnerability, but mapping of most of these sites is incomplete owing to a paucity of structural information on the full epitope in the context of the Env trimer. Here, a crystal structure of the soluble BG505 SOSIP gp140 trimer at 4.6 Å resolution with the bNAbs 8ANC195 and PGT128 reveals additional interactions in comparison to previous antibody-gp120 structures. For 8ANC195, in addition to previously documented interactions with gp120, a substantial interface with gp41 is now elucidated that includes extensive interactions with the N637 glycan. Surprisingly, removal of the N637 glycan did not impact 8ANC195 affinity, suggesting that the antibody has evolved to accommodate this glycan without loss of binding energy. PGT128 indirectly affects the N262 glycan by a domino effect, in which PGT128 binds to the N301 glycan, which in turn interacts with and repositions the N262 glycan, thereby illustrating the important role of neighboring glycans on epitope conformation and stability. Comparisons with other Env trimer and gp120 structures support an induced conformation for glycan N262, suggesting that the glycan shield is allosterically modified upon PGT128 binding. These complete epitopes of two broadly neutralizing antibodies on the Env trimer can now be exploited for HIV-1 vaccine design. PMID:26457433

ABSTRACT Similar to other type I fusion machines, the HIV-1 envelope glycoprotein (Env) requires proteolytic activation; specifically, cleavage of a gp160 precursor into gp120 and gp41 subunits creates an N-terminal gp41 fusion peptide and permits folding from an immature uncleaved state to a mature closed state. While the atomic-level consequences of cleavage for HIV-1 Env are still being determined, the uncleaved state is antigenically distinct from the mature closed state, and cleavage has been reported to be essential for mimicry of the mature viral spike by soluble versions of Env. Here we report the redesign of a current state-of-the-art soluble Env mimic, BG505.SOSIP, to make it cleavage independent. Specifically, we replaced the furin cleavage site between gp120 and gp41 with Gly-Ser linkers of various lengths. The resultant linked gp120-gp41 constructs, termed single-chain gp140 (sc-gp140), exhibited different levels of structural and antigenic mimicry of the parent cleaved BG505.SOSIP. When constructs were subjected to negative selection to remove subspecies recognized by poorly neutralizing antibodies, trimers of high antigenic mimicry of BG505.SOSIP could be obtained; negative-stain electron microscopy indicated these to resemble the mature closed state. Higher proportions of BG505.SOSIP-trimer mimicry were observed in sc-gp140s with linkers of 6 or more residues, with a linker length of 15 residues exhibiting especially promising traits. Overall, flexible linkages between gp120 and gp41 in BG505.SOSIP can thus substitute for cleavage, and sc-gp140s that closely mimicked the vaccine-preferred mature closed state of Env could be obtained. IMPORTANCE The trimeric HIV-1 envelope glycoprotein (Env) is the sole target of virus-directed neutralizing antibody responses and a primary focus of vaccine design. Soluble mimics of Env have proven challenging to obtain and have been thought to require proteolytic cleavage into two-component subunits, gp120 and gp41

Several series of novel banana-shaped H-bonded symmetric trimers (with two H-bonds) and asymmetric heterodimers (with one H-bond) were self-assembled by appropriate molar ratios of proton donors (H-donors) and acceptors (H-acceptors). The influences of H-bonded linking positions and aromatic ring numbers (4-8 aromatic rings in the rigid cores) as well as the chain lengths (n, m = 12 or 16, respectively, in the flexible parts) on the mesomorphism and the switching behavior of the bent-core supramolecules were evaluated and theoretically analyzed. Except for the supramolecular structures with longer rigid cores or shorter flexible chains possessing the rectangular columnar (Col(r) or B1) phase, the SmC(A)P(A) phase was revealed in most supramolecular asymmetric heterodimers and switched to the SmC(S)P(F) phase by applying electric fields. The polar smectic C phase was dominated for those with H-bonded sites apart from the core center. Interestingly, the SmA and nematic phases were observed in H-bonded asymmetric dimers with H-bonded sites close to the core center, which theoretically proved that the polar smectic C phase was disfavored due to an unfavorable bend angle (smaller than the lower limit of 110 degrees ) in the lowest-energy H-bonded conformer. Compared with the fully covalently bonded analogue, lower transition temperatures and lower threshold voltages were developed in the H-bonded asymmetric dimers with the polar smectic C phase. On the basis of the theoretical calculations of molecular modeling, the existence of polar switching behavior in the polar smectic C phase of asymmetric heterodimers was proven to be associated with their configurations with higher dipole moments and suitable bend angles. Furthermore, the lack of polar switching behavior in supramolecular symmetric trimers, which exhibited the regular SmC phase with weak electrical stabilities, was related to their configurations with smaller dipole moments and confirmed by theoretical

The induction of the isiA (CP43′) protein in iron-stressed cyanobacteria is accompanied by the formation of a ring of 18 CP43′ proteins around the photosystem I (PSI) trimer and is thought to increase the absorption cross section of PSI within the CP43′-PSI supercomplex. In contrast to these in vitro studies, our in vivo measurements failed to demonstrate any increase of the PSI absorption cross section in two strains (Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803) of iron-stressed cells. We report that iron-stressed cells exhibited a reduced capacity for state transitions and limited dark reduction of the plastoquinone pool, which accounts for the increase in PSII-related 685 nm chlorophyll fluorescence under iron deficiency. This was accompanied by lower abundance of the NADP-dehydrogenase complex and the PSI-associated subunit PsaL, as well as a reduced amount of phosphatidylglycerol. Nondenaturating polyacrylamide gel electrophoresis separation of the chlorophyll-protein complexes indicated that the monomeric form of PSI is favored over the trimeric form of PSI under iron stress. Thus, we demonstrate that the induction of CP43′ does not increase the PSI functional absorption cross section of whole cells in vivo, but rather, induces monomerization of PSI trimers and reduces the capacity for state transitions. We discuss the role of CP43′ as an effective energy quencher to photoprotect PSII and PSI under unfavorable environmental conditions in cyanobacteria in vivo. PMID:16798943

Two new proanthocyanidin trimers have been isolated from Cistus incanus herb; gallocatechin-(4α→6)-gallocatechin-(4α→8)-gallocatechin (compound 1) and epigallocatechin-3-O-gallate-(4ß→8)-epigallocatechin-3-O-gallate-(4ß→8)-gallocatechin (compound 2). The structures were determined on the basis of 1D- and 2D-NMR (HSQC, HMBC) of their peracetylated derivatives, MALDI-TOF-MS and by acid-catalysed degradation with phloroglucinol. A more abundant proanthocyanidin oligomer was also isolated, purified and its chemical constitution studied by (13)C-NMR and phloroglucinol degradation. The mean molecular weight of the polymer was estimated to be about 7 to 8 flavan-3-ol-units with a ratio of procyanidin : prodelphinidin units at 1:5, some of which are derivatised by gallic acid. Water extract and higher oligomeric proanthocyanidin fractions of C. incanus significantly inhibited TPA-induced oedema when applied topically at doses of 0.5 and 1 mg/ear in mice. Furthermore, the extracts and the pure compounds inhibited COX-1 and COX-2 activities. In addition, compound 2 exhibited an IC50 of 4.5 μM against COX-2 indicating its high selectivity towards COX-2. PMID:26414773

Polyphenols are partial metabolized to methylated conjugations in vivo, and then could modify bioavailability and bioactivity related to the uptake of parent compounds. Our previous studies have found that the antidiabetic effects of cinnamon barks are mainly related to polyphenol components, particularly A-type procyanidin trimer cinnamtannin-1 (CT1). It is necessary to understand the antidiabetic activity of methylations of CT1, nevertheless, sufficient amounts of methylated CT1 are difficult to obtain from metabolites in vivo. In this study, O-methyl derivatives of CT1 were prepared through one-pot methyl iodide reaction and isolation via column chromatography and RP-HPLC semipreparation. The structures of O-methyl substituents were determined through NMR (Nuclear Magnetic Resonance) and HPLC-ESI-MS (High-performance liquid chromatography-electrospray ionization-mass spectrometry). Five purified O-methyl substituents and 2 isomers of CT1 were obtained. Their protective effects on a palmitic acid-induced pancreatic β-cell apoptosis model were then evaluated. Results showed that the protective effects on pancreatic β-cell of O-methyl substituents were weaker than those of CT1. The results suggested that the methylation of catechol groups could be a relevant factor contributing to the decline of protective effects on pancreatic β-cell of CT1 via obstructing quinone intermediate formation and affecting antioxidant abilities. The antidiabetic effects of O-methyl derivatives of CT1 should be further determined by other antidiabetic models. PMID:27074527

An effective HIV-1 vaccine should ideally induce strong humoral and cellular immune responses that provide sterilizing immunity over a prolonged period. Current HIV-1 vaccines have failed in inducing such immunity. The viral envelope glycoprotein complex (Env) can be targeted by neutralizing antibodies to block infection, but several Env properties limit the ability to induce an antibody response of sufficient quantity and quality. We hypothesized that Env immunogenicity could be improved by embedding an immunostimulatory protein domain within its sequence. A stabilized Env trimer was therefore engineered with the granulocyte-macrophage colony-stimulating factor (GM-CSF) inserted into the V1V2 domain of gp120. Probing with neutralizing antibodies showed that both the Env and GM-CSF components of the chimeric protein were folded correctly. Furthermore, the embedded GM-CSF domain was functional as a cytokine in vitro. Mouse immunization studies demonstrated that chimeric EnvGM-CSF enhanced Env-specific antibody and T cell responses compared with wild-type Env. Collectively, these results show that targeting and activation of immune cells using engineered cytokine domains within the protein can improve the immunogenicity of Env subunit vaccines. PMID:21515681

Laser-induced near-infrared (NIR) emission spectra of neutral bismuth timer, Bi₃, embedded in solid neon matrixes at 3 K were recorded in a range 870-1670 nm. Using photoexcitation with low energy photons at 1064 nm, two emission band systems were newly identified by their origin bands at T₀ = 6600 and 8470 cm⁻¹. Accordingly, spectral assignment for three NIR emission band systems reported recently was partly revised for the one with its origin band at T₀ = 7755 cm⁻¹ and reconfirmed for the others at T₀ = 9625 and 11,395 cm⁻¹. Energy splitting by spin-orbit coupling between the pair of electronic energy levels in the ground state of bismuth trimer, Bi₃, both having a totally symmetric vibrational mode of frequency at ω(e)" = 150 cm⁻¹, was determined to be 1870 ± 1.5 cm⁻¹. Transitions from the pair of electronically excited states, locating at T₀ = 8470 and 9625 cm⁻¹ above the ground state and separated by spin–orbit coupling of 1155 cm⁻¹, have relatively long decay constants of τ ∼0.2 and ∼0.1 ms, respectively. PMID:25357154

Rotational spectra of three isotopomers of the Xe-(H2O)2 van der Waals trimer were recorded using a pulsed-nozzle, Fourier transform microwave spectrometer. Nine [nine, four] a-type and twelve [eleven, seven] b-type transitions were measured for the 132Xe-(H2O)2 [129Xe-(H2O)2, 131Xe-(H2O)2] isotopomer. The determined rotational and centrifugal distortion constants were used to extract information about the structure and vibrational motions of the complex. The nuclear quadrupole hyperfine structures due to the 131Xe (nuclear spin quantum number I=3/2) nucleus were also detected. The large value of the off-diagonal nuclear quadrupole coupling constant chiab in particular provides detailed insight into the electronic environment of the xenon atom and the orientations of the water molecules within the complex. An effective structure that best reproduces the experimental 131Xe nuclear quadrupole coupling constants is rationalized by ab initio calculations. An overall goal of this line of work is to determine how the successive solvation of a xenon atom with water molecules affects the xenon electron distribution and its intermolecular interactions. The results may provide molecular level interpretations of 129Xe NMR data from, for example, imaging experiments. PMID:17388264

The Eugenia jambolana is used in folklore medicine. Leaves of E. jambolana contain flavonoids as their active constituents which possess in vitro antiinflammatory, antioxidant and the antimicrobial activity. The aim of the present study was to investigate the antiinflammatory and antioxidant effects of a flavonoid glucoside, trimeric myricetin rhamnoside (TMR) isolated from leaves of E. jambolana. TMR was studied for antiinflammatory activity in carrageenan-induced hind paw oedema and antioxidant activity in lung by caecal ligation and puncture (CLP)-induced sepsis in mice. Results of the present study indicated that TMR significantly attenuated the oedema, myeloperoxidase (MPO), cytokines and prostaglandin levels in the paw after 5 h of carrageenan injection as compared to vehicle control. It also reduced the lung MPO, lipid peroxides, and serum nitrite plus nitrate levels and increased lung reduced glutathione levels 20 h of CLP as compared to vehicle control. Thus the results of this study concluded that the TMR appears to have potential benefits in diseases that are mediated by both inflammation and oxidative stress and support the pharmacological basis of use of E. jambolana plant as traditional herbal medicine for the treatment of inflammatory diseases. PMID:26343251

In this study the permeability of two flavanol-C-glucosides (FCglcs) and five dimeric and trimeric flavan-3-ols, namely, procyanidins (PCs), was investigated with the human colon carcinoma cell line (Caco-2) model. These compounds can be found especially in cocoa, and they are of great interest due to their assumed beneficial health effects. Transepithelial electrical resistance (TEER) and capacitance were measured online with a CellZscope device prior to and during the whole experiment to guarantee the maintenance of the barrier properties. The transport experiments with pure, single compounds (50-300 μM) from apical to basolateral side showed slight permeation of PCs A2, B2, and B5 and cinnamtannin B1 (CB1) as well as (-)-catechin-6-C-glucoside (C6Cglc) and (-)-catechin-8-C-glucoside (C8Cglc) of about 0.02-0.2% after 24 h. Transport of PC C1 could not be detected. Inhibition of P-glycoprotein (Pgp) increased the permeation of PC B2 and CB1 to the basolateral side, which indicates that Pgp counteracts the transport of these compounds. Metabolites (epicatechin, 3'- and 4'-O-epicatechin) in very small amounts were detectable only for PC B2. These are the first data concerning the permeability of flavan-3-ol-C-glucosides across the Caco-2 cell monolayer. PMID:23885956

Polycyclic aromatic hydrocarbons (PAHs) are key species encountered in a large variety of environments such as the Interstellar Medium (ISM) and in combustion media. Their UV spectroscopy and photodynamics in neutral and cationic forms are important to investigate in order to learn about their structure, formation mechanisms, and reactivity. Here, we report an experimental photoelectron-photoion coincidence study of a prototypical PAH molecule, coronene, and its small clusters, in a molecular beam using the vacuum ultraviolet (VUV) photons provided by the SOLEIL synchrotron facility. Mass-selected high resolution threshold photoelectron (TPES) and total ion yield spectra were obtained and analyzed in detail. Intense series of autoionizing resonances have been characterized as originating from the monomer, dimer, and trimer neutral species, which may be used as spectral fingerprints for their detection in the ISM by VUV absorption spectroscopy. Finally, a full description of the electronic structure of the monomer cation was made and discussed in detail in relation to previous spectroscopic optical absorption data. Tentative vibrational assignments in the near-threshold TPES spectrum of the monomer have been made with the support of a theoretical approach based on density functional theory.

Acinetobacter sp. Tol 5 exhibits an autoagglutinating nature and noteworthy adhesiveness to various abiotic surfaces from hydrophobic plastics to hydrophilic glass and stainless steel. Although previous studies have suggested that bacterionanofibers on Tol 5 cells are involved in the adhesive phenotype of Tol 5, the fiber that directly mediates Tol 5 adhesion has remained unknown. Here, we present a new member of trimeric autotransporter adhesins designated AtaA, which we discovered by analyzing a less adhesive mutant of Tol 5, T1, obtained by transposon mutagenesis. AtaA forms thinner and shorter nanofibers than fimbriae on Tol 5 cells. We performed target disruption of ataA by allelic marker exchange, and the resulting ΔataA strain was complemented with ataA on the Escherichia coli-Acinetobacter shuttle vector, which was newly constructed. These results proved that AtaA is essential for Tol 5’s autoagglutinating nature and high adhesiveness to surfaces of various materials. In addition, the adhesiveness to solid surfaces mediated by AtaA is notably higher than that mediated by YadA of Yersinia enterocolitica WA-314. Moreover, and importantly, these characteristics can be conferred to the non-adhesive, non-agglutinating bacterium Acinetobacter sp. ADP1 in trans by transformation with ataA, with expected applications to microbial immobilization. PMID:23155410

Model-building studies were carried out on the trimer AUA. Bulge-out structures which allow incorporation into a continuous RNA helix were generated and energy-minimized. All geometrical features obtained by previous NMR studies on purine-pyrimidine-purine sequences are accounted for in these models. One of the models was used to fit into a double helical fragment. Only minor changes were necessary to construct a central bulge-out in an otherwise intact duplex. NMR and model-building studies were performed on the duplex (CUGGUGCGG).(CCGCCCAG) which contains an unpaired uridine residue. NOE data, chemical-shift profiles and imino-proton resonances provided evidence that the extra U is bulged out of the duplex. The relatively small dispersion in 31P chemical shifts (approximately equal to 0.7 ppm) indicate the absence of t/g or g/t combinations for the phosphodiester angles zeta/alpha. An energy-minimized model of the duplex, which fits the present collection of data, is presented. PMID:3387215

Vascular endothelial growth factor receptor 2 (VEGFR2)-mediated signaling is the key rate-limiting step in angiogenesis. VEGFR2 serves as the most important target of anti-angiogenic therapy for cancers. Single-chain trimer (SCT) comprising antigen peptide, β2-microglobulin (β2m), and major histocompatibility complex (MHC) class I heavy chain was a particularly powerful strategy involved in the increase of the potency of DNA vaccine against tumors and infections. In the present study, we constructed an SCT-encoding VEGFR2 antigen peptide [aa400-408, also known as kinase insert domain-containing receptor (KDR2)], β2m, and mouse MHC class I heavy chain H-2Db [pcDNA3.1(+)-KDR2-β2m-H-2Db, or SCT-KDR2]. The constructed SCT-KDR2 DNA was efficiently expressed in the human A293 embryonic kidney cell line. Intradermal immunization of C57BL/6 mice with SCT-KDR2 DNA was able to successfully break self-immunological tolerance and induce robust cytotoxic T‑lymphocyte (CTL) response to VEGFR2, leading to marked suppression of tumor cell‑induced angiogenesis and metastasis in murine models of B16 melanoma and 3LL Lewis lung carcinoma. Taken together, the results showed that VEGFR2-targeted SCT vaccination is an effective modality that can be utilized in anti-angiogenic active immunotherapy for various types of cancer. PMID:25739076

Background: In cycling tumour cells, the binary cyclin-dependent kinase Cdk4/cyclin D or Cdk2/cyclin E complex is inhibited by p21 following DNA damage to induce G1 cell-cycle arrest. However, it is not known whether other proteins are also recruited within Cdk complexes, or their role, and this was investigated. Methods: Ovarian A2780 tumour cells were exposed to the platinum-based antitumour agent 1R,2R-diaminocyclohexane(trans-diacetato)(dichloro)platinum(IV) (DAP), which preferentially induces G1 arrest in a p21-dependent manner. The Cdk complexes were analysed by gel filtration chromatography, immunoblot and mass spectrometry. Results: The active forms of Cdk4 and Cdk2 complexes in control tumour cells have a molecular size of ∼140 kDa, which increased to ∼290 kDa when inhibited following G1 checkpoint activation by DAP. Proteomic analysis identified Cdk, cyclin, p21 and proliferating cell nuclear antigen (PCNA) in the inhibited complex, and biochemical studies provided unequivocal evidence that the increase in ∼150 kDa of the inhibited complex is consistent with p21-dependent recruitment of PCNA as a trimer, likely bound to three molecules of p21. Although p21 alone was sufficient to inhibit the Cdk complex, PCNA was critical for stabilising p21. Conclusion: G1 Cdk complexes inhibited by p21 also recruit PCNA, which inhibits degradation and, thereby, prolongs activity of p21 within the complex. PMID:24104967

The adhesion of bacterial pathogens to host cells is an event that determines infection, and ultimately invasion and intracellular multiplication. Several evidences have recently shown that this rule is also truth for the intracellular pathogen Brucella. Brucella suis displays the unipolar BmaC and BtaE adhesins, which belong to the monomeric and trimeric autotransporter (TA) families, respectively. It was previously shown that these adhesins are involved in bacterial adhesion to host cells and components of the extracellular matrix (ECM). In this work we describe the role of a new member of the TA family of B. suis (named BtaF) in the adhesive properties of the bacterial surface. BtaF conferred the bacteria that carried it a promiscuous adhesiveness to various ECM components and the ability to attach to an abiotic surface. Furthermore, BtaF was found to participate in bacterial adhesion to epithelial cells and was required for full virulence in mice. Similar to BmaC and BtaE, the BtaF adhesin was expressed in a small subpopulation of bacteria, and in all cases, it was detected at the new pole generated after cell division. Interestingly, BtaF was also implicated in the resistance of B. suis to porcine serum. Our findings emphasize the impact of TAs in the Brucella lifecycle. PMID:24236157

The papillomavirus E1 protein is a multifunctional initiator protein responsible for preparing the viral DNA template for initiation of DNA replication. The E1 protein encodes two DNA binding activities that are required for initiation of DNA replication. A well-characterized sequence-specific DNA binding activity resides in the E1 DBD and is used to tether E1 to the papillomavirus ori. A non-sequence-specific DNA binding activity is also required for formation of the E1 double trimer (DT) complex, which is responsible for the local template melting that precedes loading of the E1 helicase. This DNA binding activity is very poorly understood. We use a structure-based mutagenesis approach to identify residues in the E1 helicase domain that are required for the non-sequence-specific DNA binding and DT formation. We found that three groups of residues are involved in nonspecific DNA binding: the E1 β-hairpin structure containing R505, K506, and H507; a hydrophobic loop containing F464; and a charged loop containing K461 together generate the binding surface involved in nonspecific DNA binding. These residues are well conserved in the T antigens from the polyomaviruses, indicating that the polyomaviruses share this nonspecific DNA binding activity. PMID:20147403

The Type VI secretion system (T6SS) is a macromolecular machine that mediates bacteria-host or bacteria-bacteria interactions. The T6SS core apparatus assembles from 13 proteins that form two sub-assemblies: a phage-like complex and a trans-envelope complex. The Hcp, VgrG, TssE, and TssB/C subunits are structurally and functionally related to components of the tail of contractile bacteriophages. This phage-like structure is thought to be anchored to the membrane by a trans-envelope complex composed of the TssJ, TssL, and TssM proteins. However, how the two sub-complexes are connected remains unknown. Here we identify TssK, a protein that establishes contacts with the two T6SS sub-complexes through direct interactions with TssL, Hcp, and TssC. TssK is a cytoplasmic protein assembling trimers that display a three-armed shape, as revealed by TEM and SAXS analyses. Fluorescence microscopy experiments further demonstrate the requirement of TssK for sheath assembly. Our results suggest a central role for TssK by linking both complexes during T6SS assembly. PMID:23921384

Polycyclic aromatic hydrocarbons (PAHs) are key species encountered in a large variety of environments such as the Interstellar Medium (ISM) and in combustion media. Their UV spectroscopy and photodynamics in neutral and cationic forms are important to investigate in order to learn about their structure, formation mechanisms, and reactivity. Here, we report an experimental photoelectron-photoion coincidence study of a prototypical PAH molecule, coronene, and its small clusters, in a molecular beam using the vacuum ultraviolet (VUV) photons provided by the SOLEIL synchrotron facility. Mass-selected high resolution threshold photoelectron (TPES) and total ion yield spectra were obtained and analyzed in detail. Intense series of autoionizing resonances have been characterized as originating from the monomer, dimer, and trimer neutral species, which may be used as spectral fingerprints for their detection in the ISM by VUV absorption spectroscopy. Finally, a full description of the electronic structure of the monomer cation was made and discussed in detail in relation to previous spectroscopic optical absorption data. Tentative vibrational assignments in the near-threshold TPES spectrum of the monomer have been made with the support of a theoretical approach based on density functional theory.

Salmonella enterica is a major cause of morbidity worldwide and mortality in children and immunocompromised individuals in sub-Saharan Africa. Outer membrane proteins of Salmonella are of significance because they are at the interface between the pathogen and the host, they can contribute to adherence, colonization, and virulence, and they are frequently targets of antibody-mediated immunity. In this study, the properties of SadA, a purported trimeric autotransporter adhesin of Salmonella enterica serovar Typhimurium, were examined. We demonstrated that SadA is exposed on the Salmonella cell surface in vitro and in vivo during infection of mice. Expression of SadA resulted in cell aggregation, biofilm formation, and increased adhesion to human intestinal Caco-2 epithelial cells. Immunization of mice with folded, full-length, purified SadA elicited an IgG response which provided limited protection against bacterial challenge. When anti-SadA IgG titers were enhanced by administering alum-precipitated protein, a modest additional protection was afforded. Therefore, despite SadA having pleiotropic functions, it is not a dominant, protective antigen for antibody-mediated protection against Salmonella. PMID:21859856

Background. A key missing element in the development of a successful human immunodeficiency virus (HIV) vaccine is an immunogen that can generate broadly cross-neutralizing antibodies against primary isolates of the virus. Methods. This phase 1 clinical trial employed a DNA prime and subunit envelope protein boost in an attempt to generate cellular and humoral immune responses that might be desirable in a protective HIV vaccine. Priming was performed via intramuscular injection with gag and env DNA adsorbed to polylactide coglycolide microspheres, followed by boosting with a recombinant trimeric envelope (Env) glycoprotein delivered in MF59 adjuvant. Results. The DNA prime and protein boost were generally safe and well-tolerated. Env-specific CD4+ cellular responses were generated that were predominantly detected after Env protein boosting. Neutralizing antibody responses against the homologous SF162 viral isolate were remarkably strong and were present in the majority of vaccine recipients, including a strong response against CD4-induced epitopes on gp120. Despite the promising potency of this vaccine approach, neutralization breadth against heterologous tier 2 strains of HIV-1 was minimal. Conclusions. Potent neutralization against neutralization-sensitive strains of HIV is achievable in humans through a DNA prime, recombinant oligomeric Env protein boost regimen. Eliciting substantial breadth of neutralization remains an elusive goal. Clinical Trials Registration. NCT00073216. PMID:21451004

Vibrational energy relaxation (VER) in the CH stretching region of benzene dimer (Bz_2) and trimer (Bz_3) has been studied by IR-UV pump-probe spectroscopy in supersonic beams. Firstly, we investigated isotope-substituted hd heterodimer, where h=C_6H_6 and d=_6D_6, because the Stem and Top sites in the hd dimer can be site-selectively excited, different from hh homodimer. The two h(stem)d(top) and h(top)d(stem) isomers show remarkable difference in the lifetimes of intracluster vibrational energy redistribution (IVR). In the transient UV spectra, we observed a broad electronic transition due to the bath modes. The time evolutions of the bath modes can be described by a three step VER model involving IVR and vibrational predissociation (VP). This model was also confirmed by the observed rise profile of the Bz fragment. Secondly, we investigated hh homodimer. The hh homodimer shows the stepwise VER process with time constants similar to those of the hd dimer, suggesting a very weak excitation-exchange coupling of the vibrations between the two sites of the hh dimer. Finally, we found that Bz_3 also exhibits the stepwise VER process, though each step is faster than Bz_2.

Polycyclic aromatic hydrocarbons (PAHs) are key species encountered in a large variety of environments such as the Interstellar Medium (ISM) and in combustion media. Their UV spectroscopy and photodynamics in neutral and cationic forms are important to investigate in order to learn about their structure, formation mechanisms, and reactivity. Here, we report an experimental photoelectron-photoion coincidence study of a prototypical PAH molecule, coronene, and its small clusters, in a molecular beam using the vacuum ultraviolet (VUV) photons provided by the SOLEIL synchrotron facility. Mass-selected high resolution threshold photoelectron (TPES) and total ion yield spectra were obtained and analyzed in detail. Intense series of autoionizing resonances have been characterized as originating from the monomer, dimer, and trimer neutral species, which may be used as spectral fingerprints for their detection in the ISM by VUV absorption spectroscopy. Finally, a full description of the electronic structure of the monomer cation was made and discussed in detail in relation to previous spectroscopic optical absorption data. Tentative vibrational assignments in the near-threshold TPES spectrum of the monomer have been made with the support of a theoretical approach based on density functional theory. PMID:25362317

Spin-spin correlations and microscopic origin of net magnetization in the spin-1 trimer chain compound CaNi3P4O14 have been investigated by powder neutron diffraction. The present study reveals a three-dimensional long-range magnetic ordering below 16 K where the magnetic structure consists of ferromagnetic trimers that are coupled ferromagnetically along the spin-chain direction (b axis). The moment components along the a and c axes arrange antiferromagnetically. Our study establishes that the uncompensated moment components along the b axis (mb) result in a net magnetization per unit cell. The magnetic structure, determined in the present study, is in agreement with the results of recent first-principles calculation; however, it is in contrast to a fascinating experimental prediction of ferrimagnetic ordering based on the periodicity of the exchange interactions in CaNi3P4O14 . Our study also confirms the presence of broad diffuse magnetic scattering, due to one-dimensional short-range spin-spin correlations, over a wide temperature range below ˜50 K down to a temperature well below the Tc. Total neutron scattering analysis by the reverse Monte Carlo (RMC) method reveals that the dominating spin-spin correlation above Tc is ferromagnetic and along the b axis. The nearest-neighbor spin-spin correlations along the a and c axes are found to be weakly antiferromagnetic. The nature of the trimer spin structure of the short-range ordered state (above Tc) is similar to that of the 3D long-range ordered state (below Tc). The present investigation of microscopic nature of the magnetic ground state also explains the condition required for the 1/3 magnetization plateau to be observed in the trimer spin chains. In spite of the S =1 trimer chain system, the present compound CaNi3P4O14 is found to be a good realization of a three-dimensional magnet below Tc=16 K with full ordered moment values of ˜2 μB/Ni2 + (1.98 and 1.96 μB/Ni2 + for two Ni sites, respectively) at 1.5 K.

Solvothermal reactions of CuI, 1,4-diazabicyclo[2.2.2]octane (DABCO), and HI in an ethanol solution at 140 °C/150 °C for 7 days resulted in two 24-membered-ring-based layered semiconducting iodocuprate open-network polymorphs formulated as [deDABCO]2[meDABCO]Cu11I17 (deDABCO = N,N'-diethyl-1,4-diazabicyclo[2.2.2] octane and meDABCO = N-methyl-N'-ethyl-1,4-diazabicyclo[2.2.2]octane). The deDABCO and meDABCO templates were in situ generated via alkylation of DABCO during solvothermal reactions. The formation of layered Cu11I17(6-) polymorphs can be rationalized via analyses of hierarchical building units. There are four hierarchical building units in polymorphs, namely, primary CuI3 triangle and CuI4 tetrahedron, secondary Cu3I7 trimer and Cu4I8 tetramer, tertiary Cu6I12 hexamer, and quaternary Cu12I22 dodecamer. The trimeric Cu3I7 secondary building unit (SBU) is constructed by three edge-shared CuI4 tetrahedra, while the tetrameric Cu4I8 SBU with an inversion center is formed by edge-shared two CuI3 triangles and two CuI4 tetrahedra. Two Cu3I7 SBUs are fused together via the sharing of two iodine atoms to form a Cu6I12 tertiary building unit (TBU), and two TBUs are further fused via the sharing of two iodine atoms into a Cu12I22 quaternary building unit (QBU). In colorless polymorph 1, each Cu3I7 SBU is connected to three neighbors via one Cu4I8 and two Cu6I12 linkers to form a 6,3-connected layer with 24-membered ring window. Different from 1, each Cu6I12 TBU in yellowish polymorph 2 is connected to four neighbors via two Cu4I8 and two Cu12I22 linkers to form a (4,4) topological layer also with 24-membered-ring window. These two compounds are very rare examples of copper halide polymorphs that exhibit similar local coordination geometries of copper(I) but different layered open networks. Electrical conductivity, band structure calculation, and UV-vis diffuse-reflectance spectrometry indicate that 1 and 2 are potential semiconductor materials, and the performance

Vaccination is the most cost-effective way to control infectious diseases in cattle. However, many infectious diseases leading to severe economical losses worldwide still remain for which a really effective and safe vaccine is not available. These diseases are most often due to intracellular pathogens such as bacteria or viruses, which are, by their localization, protected from antibiotics and/or CD4(+) T cell-dependent humoral responses. We therefore postulated that strategies leading to induction of not only CD4(+) T cell responses but also CD8(+) cytotoxic T lymphocyte (CTL) responses against infected cells should be privileged in the development of new vaccines against problematic intracellular pathogens in bovines. CD40 signaling in antigen-presenting cells may lead to the induction of robust CD4-independent CTL responses and several studies, especially in mice, have used CD40 stimulation to promote CD8(+) T cell-mediated immunity. For example, we have recently shown that immunization of mice with heat-killed Staphylococcus aureus (HKSA) and agonistic anti-CD40 monoclonal antibodies elicits strong CTL responses capable of protecting mice from subsequent staphylococcal mastitis. Unfortunately, there is at present no tool available to efficiently stimulate CD40 in cattle. In this study, we therefore first produced a soluble recombinant trimeric form of the natural bovine CD40 ligand (sboCD40LT). We then observed that sboCD40LT was able to potently stimulate bovine cells in vitro. Finally, we provide evidence that immunization of cows with sboCD40LT combined with HKSA was able to significantly increase the number of both HKSA-specific CD4(+) and CD8(+) T cells in the draining lymph nodes. In conclusion, we suggest that this new molecular tool could help in the development of vaccine strategies against bovine diseases caused by intracellular pathogens. PMID:26553560

A spontaneous mutation termed bilateral wasting kidneys (bwk) was identified in a colony of NONcNZO recombinant inbred mice. These mice exhibit a rapid increase of urinary albumin at an early age associated with glomerulosclerosis, interstitial nephritis, and tubular atrophy. The mutation was mapped to a location on Chromosome 1 containing the Col4a3 and Col4a4 genes, for which mutations in the human orthologs cause the hereditary nephritis Alport syndrome. DNA sequencing identified a G to A mutation in the conserved GT splice donor of Col4a4 intron 30, resulting in skipping of exon 30 but maintaining the mRNA reading frame. Protein analyses showed that mutant collagen α3α4α5(IV) trimers were secreted and incorporated into the glomerular basement membrane (GBM), but levels were low, and GBM lesions typical of Alport syndrome were observed. Moving the mutation into the more renal damage-prone DBA/2J and 129S1/SvImJ backgrounds revealed differences in albuminuria and its rate of increase, suggesting an interaction between the Col4a4 mutation and modifier genes. This novel mouse model of Alport syndrome is the only one shown to accumulate abnormal collagen α3α4α5(IV) in the GBM, as also found in a subset of Alport patients. These mice will be valuable for testing potential therapies, for understanding abnormal collagen IV structure and assembly, for gaining better insights into the mechanisms leading to Alport syndrome and to the variability in the age of onset and associated phenotypes. PMID:24522496

Due to its proximity of Hg(II) atoms, electron-withdrawing properties and inherent accessibility to electrophilic sites on the molecular surface, trimeric perfluoro-ortho-phenylenemercury, (o-C6F4Hg)3, has demonstrated a capacity to form supramolecular adducts with a variety of neutral and anionic substrates. Often within these complexes the Lewis acid, (o-C6F4Hg)3, interacts with a Lewis base rather than itself in the solid state via various supramolecular interactions. Among these, perfluorophenyl-perfluorophenyl interactions have been utilized in the construction of various supramolecular materials; however, within these molecular complexes, this category of non-covalent interaction is not often observed. Even though these perfluorophenyl-perfluorophenyl interactions have been used to produce new materials, their overall strength has not been generally reported in the literature. In this contribution, we highlight not only the synthesis, structural and spectroscopic properties of a novel binary supramolecular adduct between (o-C6F4Hg)3 and 4-chlorobenzaldehyde (4-ClBA) [(o-C6F4Hg)3(4-ClBA)] 1, but also report on the overall strength of the perfluorophenyl-perfluorophenyl interaction energies determined by means of computational chemistry. The carbonyl group of the 4-ClBA substrate was found to interact with all three mercury atoms within (o-C6F4Hg)3 via Hg&ctdot;O contacts. An infrared spectroscopic analysis of 1 demonstrated a lower wavenumber for the carbonyl stretching frequency when compared to that for the free substrate confirming the presence of these Hg&ctdot;O interactions.

A novel algorithm for performing configuration interaction (CI) calculations using non-orthogonal orbitals is introduced. In the new algorithm, the explicit calculation of the Hamiltonian matrix is replaced by the direct evaluation of the Hamiltonian matrix times a vector, which allows expressing the CI-vector in a bi-orthonormal basis, thereby drastically reducing the computational complexity. A new non-orthogonal orbital optimization method that employs exponential mappings is also described. To allow non-orthogonal transformations of the orbitals, the standard exponential mapping using anti-symmetric operators is supplemented with an exponential mapping based on a symmetric operator in the active orbital space. Expressions are obtained for the orbital gradient and Hessian, which involve the calculation of at most two-body density matrices, thereby avoiding the time-consuming calculation of the three- and four-body density matrices of the previous approaches. An approach that completely avoids the calculation of any four-body terms with limited degradation of convergence is also devised. The novel methods for non-orthogonal configuration interaction and orbital optimization are applied to the chromium dimer and trimer. For internuclear distances that are typical for chromium clusters, it is shown that a reference configuration consisting of optimized singly occupied active orbitals is sufficient to give a potential curve that is in qualitative agreement with complete active space self-consistent field (CASSCF) calculations containing more than 500 × 106 determinants. To obtain a potential curve that deviates from the CASSCF curve by less than 1 mHartree, it is sufficient to add single and double excitations out from the reference configuration.

For most paramyxoviruses, virus type-specific interaction between fusion (F) protein and attachment protein (hemagglutinin-neuraminidase [HN], hemagglutinin [H], or glycoprotein [G]) is a prerequisite for mediating virus-cell fusion and cell-cell fusion. Our previous cell-cell fusion assay using the chimeric F proteins of human parainfluenza virus 2 (HPIV2) and simian virus 41 (SV41) suggested that the middle region of the HPIV2 F protein contains the site(s) that determines its specificity for the HPIV2 HN protein. In the present study, we further investigated the sites of the F protein that could be critical for determining the HN protein specificity. By analyzing the reported structure of the F protein of parainfluenza virus 5 (PIV5), we found that four major domains (M1, M2, M3, and M4) and five minor domains (A to E) in the middle region of the PIV5 F protein were exposed on the trimer surface. We then replaced these domains with the SV41 F counterparts individually or in combination and examined whether the resulting chimeras could mediate cell-cell fusion when coexpressed with the SV41 HN protein. The results showed that a chimera designated M(1+2), which harbored SV41 F-derived domains M1 and M2, mediated cell-cell fusion with the coexpressed SV41 HN protein, suggesting that these domains are involved in determining the HN protein specificity. Intriguingly, another chimera which harbored the SV41 F-derived domain B in addition to domains M1 and M2 showed increased specificity for the SV41 HN protein compared to that of M(1+2), although it was capable of mediating cell-cell fusion by itself. PMID:21270148

A novel algorithm for performing configuration interaction (CI) calculations using non-orthogonal orbitals is introduced. In the new algorithm, the explicit calculation of the Hamiltonian matrix is replaced by the direct evaluation of the Hamiltonian matrix times a vector, which allows expressing the CI-vector in a bi-orthonormal basis, thereby drastically reducing the computational complexity. A new non-orthogonal orbital optimization method that employs exponential mappings is also described. To allow non-orthogonal transformations of the orbitals, the standard exponential mapping using anti-symmetric operators is supplemented with an exponential mapping based on a symmetric operator in the active orbital space. Expressions are obtained for the orbital gradient and Hessian, which involve the calculation of at most two-body density matrices, thereby avoiding the time-consuming calculation of the three- and four-body density matrices of the previous approaches. An approach that completely avoids the calculation of any four-body terms with limited degradation of convergence is also devised. The novel methods for non-orthogonal configuration interaction and orbital optimization are applied to the chromium dimer and trimer. For internuclear distances that are typical for chromium clusters, it is shown that a reference configuration consisting of optimized singly occupied active orbitals is sufficient to give a potential curve that is in qualitative agreement with complete active space self-consistent field (CASSCF) calculations containing more than 500 × 10(6) determinants. To obtain a potential curve that deviates from the CASSCF curve by less than 1 mHartree, it is sufficient to add single and double excitations out from the reference configuration. PMID:26395682

The C-terminal oligomerization domain of chicken cartilage matrix protein is a trimeric coiled coil comprised of three identical 43-residue chains. NMR spectra of the protein show equivalent magnetic environments for each monomer, indicating a parallel coiled coil structure with complete threefold symmetry. Sequence-specific assignments for 1H-, 15N-, and 13C-NMR resonances have been obtained from 2D 1H NOESY and TOCSY spectra, and from 3D HNCA, 15N NOESY-HSQC, and HCCH-TOCSY spectra. A stretch of alpha-helix encompassing five heptad repeats (35 residues) has been identified from intra-chain HN-HN and HN-H alpha NOE connectivities. 3JHNH alpha coupling constants, and chemical shift indices. The alpha-helix begins immediately downstream of inter-chain disulfide bonds between residues Cys 5 and Cys 7, and extends to near the C-terminus of the molecule. The threefold symmetry of the molecule is maintained when the inter-chain disulfide bonds that flank the N-terminus of the coiled coil are reduced. Residues Ile 21 through Glu 36 show conserved chemical shifts and NOE connectivities, as well as strong protection from solvent exchange in the oxidized and reduced forms of the protein. By contrast, residues Ile 10 through Val 17 show pronounced chemical shift differences between the oxidized and reduced protein. Strong chemical exchange NOEs between HN resonances and water indicate solvent exchange on time scales faster than 10 s, and suggests a dynamic fraying of the N-terminus of the coiled coil upon reduction of the disulfide bonds. Possible roles for the disulfide crosslinks of the oligomerization domain in the function of cartilage matrix protein are proposed. PMID:9260286

Human T-cell leukemia virus type 1 (HTLV-1) entry into cells is dependent upon the viral envelope glycoprotein-catalyzed fusion of the viral and cellular membranes. Following receptor activation of the envelope, the transmembrane glycoprotein (TM) is thought to undergo a series of fusogenic conformational transitions through a rod-like prehairpin intermediate to a compact trimer-of-hairpins structure. Importantly, synthetic peptides that interfere with the conformational changes of TM are potent inhibitors of membrane fusion and HTLV-1 entry, suggesting that TM is a valid target for antiviral therapy. To assess the utility of TM as a vaccine target and to explore further the function of TM in HTLV-1 pathogenesis, we have begun to examine the immunological properties of TM. Here we demonstrate that a recombinant trimer-of-hairpins form of the TM ectodomain is strongly immunogenic. Monoclonal antibodies raised against the TM immunogen specifically bind to trimeric forms of TM, including structures thought to be important for membrane fusion. Importantly, these antibodies recognize the envelope on virally infected cells but, surprisingly, fail to neutralize envelope-mediated membrane fusion or infection by pseudotyped viral particles. Our data imply that, even in the absence of overt membrane fusion, there are multiple forms of TM on virally infected cells and that some of these display fusion-associated structures. Finally, we demonstrate that many of the antibodies possess the ability to recruit complement to TM, suggesting that envelope-derived immunogens capable of eliciting a combination of neutralizing and complement-fixing antibodies would be of value as subunit vaccines for intervention in HTLV infections. PMID:17376912

In the present study, the mechanism of action and molecular basis for the activity of the first class of selective inhibitors of the human excitatory amino acid transporter subtype 1 (EAAT1) and its rodent ortholog GLAST are elucidated. The previously reported specificity of UCPH-101 and UCPH-102 for EAAT1 over EAAT2 and EAAT3 is demonstrated to extend to the EAAT4 and EAAT5 subtypes as well. Interestingly, brief exposure to UCPH-101 induces a long-lasting inactive state of EAAT1, whereas the inhibition exerted by closely related analogs is substantially more reversible in nature. In agreement with this, the kinetic properties of UCPH-101 unblocking of the transporter are considerably slower than those of UCPH-102. UCPH-101 exhibits noncompetitive inhibition of EAAT1, and its binding site in GLAST has been delineated in an elaborate mutagenesis study. Substitutions of several residues in TM3, TM4c, and TM7a of GLAST have detrimental effects on the inhibitory potency and/or efficacy of UCPH-101 while not affecting the pharmacological properties of (S)-glutamate or the competitive EAAT inhibitor TBOA significantly. Hence, UCPH-101 is proposed to target a predominantly hydrophobic crevice in the "trimerization domain" of the GLAST monomer, and the inhibitor is demonstrated to inhibit the uptake through the monomer that it binds to exclusively and not to affect substrate translocation through the other monomers in the GLAST trimer. The allosteric mode of UCPH-101 inhibition underlines the functional importance of the trimerization domain of the EAAT and demonstrates the feasibility of modulating transporter function through ligand binding to regions distant from its "transport domain." PMID:23325245

Microwave spectra have been recorded for the C_{3v} symmetric complexes Kr-SO_{3} and Kr-SO_{3}-CO. The Kr-S distances are 3.438(3) Å in Kr-SO_{3} and 3.488(6) Å in Kr-SO_{3}-CO. Thus, the addition of CO to Kr-SO_{3} increases the Kr-S distance by 0.050(9) Å. In contrast, the C-S distance in the trimer, 2.871(9) Å, is the same as that previously determined for SO_{3}-CO to within the estimated uncertainties. Observed values of the ^{83}Kr nuclear quadrupole coupling constants provide direct probes of the electric field gradient at the Kr nucleus. We find that, although the Kr and CO in the trimer are on opposite sides of the SO_{3} and are thus not in direct contact, the addition of CO to Kr-SO_{3} reduces the electric field gradient at the Kr nucleus by 18%. Calculations using the Block Localized Wavefunction decomposition method are used to understand the physical origins of this change. While the magnitudes of both the electric field and the electric field gradient at the Kr nucleus decrease upon addition of the CO to Kr-SO_{3}, the changes arise from different and rather complex combinations of geometrical distortion, electrostatic, polarization, and electron transfer effects. For the electric field gradient, polarization and structural change in the Kr-SO_{3} make the primary contributions while for the electric field itself, the change in the electrostatic contribution has the largest effect. The calculated binding energies are additive, with that of the trimer very nearly equal to the sum of the binding energies of Kr-SO_{3} and SO_{3}-CO.

Background Highly pathogenic avian influenza virus (HPAIV) causes a highly contagious often fatal disease in poultry, resulting in significant economic losses in the poultry industry. HPAIV H5N1 also poses a major public health threat as it can be transmitted directly from infected poultry to humans. One effective way to combat avian influenza with pandemic potential is through the vaccination of poultry. Several live vaccines based on attenuated Newcastle disease virus (NDV) that express influenza hemagglutinin (HA) have been developed to protect chickens or mammalian species against HPAIV. However, the zoonotic potential of NDV raises safety concerns regarding the use of live NDV recombinants, as the incorporation of a heterologous attachment protein may result in the generation of NDV with altered tropism and/or pathogenicity. Methodology/Principal Findings In the present study we generated recombinant NDVs expressing either full length, membrane-anchored HA of the H5 subtype (NDV-H5) or a soluble trimeric form thereof (NDV-sH53). A single intramuscular immunization with NDV-sH53 or NDV-H5 fully protected chickens against disease after a lethal challenge with H5N1 and reduced levels of virus shedding in tracheal and cloacal swabs. NDV-sH53 was less protective than NDV-H5 (50% vs 80% protection) when administered via the respiratory tract. The NDV-sH53 was ineffective in mice, regardless of whether administered oculonasally or intramuscularly. In this species, NDV-H5 induced protective immunity against HPAIV H5N1, but only after oculonasal administration, despite the poor H5-specific serum antibody response it elicited. Conclusions/Significance Although NDV expressing membrane anchored H5 in general provided better protection than its counterpart expressing soluble H5, chickens could be fully protected against a lethal challenge with H5N1 by using the latter NDV vector. This study thus provides proof of concept for the use of recombinant vector vaccines

Apolipoprotein A-I (apoA-I) exerts many potentially anti-atherogenic properties and is therefore attractive for prevention and therapy of coronary heart disease. Since induction of apoA-I production by small molecules has turned out as difficult, application of exogenous apoA-I is pursued as an alternative therapeutic option. To counteract fast renal filtration of apoA-I, a trimeric high-molecular weight variant of apoA-I (TripA) was produced by recombinant technology. We compared TripA and apoA-I for important properties in reverse cholesterol transport. Reconstituted high-density lipoproteins (rHDL) containing TripA or apoA-I together with palmitoyl-2-oleyl-phosphatidylcholine (POPC) differed slightly by size. Compared to apoA-I, TripA activated lecithin:cholesterol acyltransferase (LCAT) with similar maximal velocity but concentration leading to half maximal velocity was slightly reduced (K(m)=2.1±0.3μg/mL vs. 0.59±0.06μg/mL). Both in the lipid-free form and as part of rHDL, TripA elicited cholesterol efflux from THP1-derived macrophages with similar kinetic parameters and response to liver-X-receptor activation as apoA-I. Lipid-free TripA is bound and transported by aortic endothelial cells through mechanisms which are competed by apoA-I and TripA and inhibited by knock-down of ATP-binding cassette transporter (ABC) A1. Pre-formed TripA/POPC particles were bound and transported by endothelial cells through mechanisms which are competed by excess native HDL as well as reconstituted HDL containing either apoA-I or TripA and which involve ABCG1 and scavenger receptor B1 (SR-BI). In conclusion, apoA-I and TripA show similar in vitro properties which are important for reverse cholesterol transport. These findings are important for further development of TripA as an anti-atherosclerotic drug. PMID:21930241

The structural and magnetic properties of mixed Pt-Co and Pt-Fe trimers and tetramers in the gas-phase and supported on a free-standing graphene layer have been calculated using density-functional theory. The influence of the strong magnetic moments of the 3d atoms on the Pt atoms and the influence of the strong spin-orbit coupling contributed by the Pt atoms on the 3d atoms have been studied in detail. All mixed trimers form isocele triangles in the gas-phase. On a graphene layer the structure is influenced by the strong binding of the 3d atoms, leading to an asymmetric configuration for Pt-rich and more symmetric structures for 3d-rich clusters. The magnetic anisotropy energy defined as the energy difference for easy and hard magnetization directions varies between 5 and 13 meV/atom for the free trimers, but is strongly reduced to values between 0.7 and 6.6 meV/atom for the graphene-supported clusters. The saddle-point energy representing the barrier against magnetization reversal is on average 3 meV/atom for free trimers, it is reduced to 2 meV/atom for the more symmetric PtCo(Fe)(2) clusters, and to only about 0.3 meV/atom for the asymmetric Pt(2)Co(Fe) cluster on graphene. For the mixed tetramers the strong magnetism stabilizes a flat geometric structure, except for Pt(3)Co which forms a distorted trigonal pyramid. The geometry of the graphene-supported tetramers is very different due to the requirement of a good match to the substrate. Large magnetic anisotropy energies are found for free Pt(3)Co where the change of the magnetization direction also induces a transition from a high- to a low-moment magnetic isomer. For all other free tetramers the magnetic anisotropy energy ranges between 3 to 5 meV/atom only, it is further reduced to 0.4 to 3.8 meV/atom for the graphene-supported tetramers. The reduction is strongest for Pt(3)Fe/graphene because of the asymmetric structure of the adsorption complex. The barriers against magnetization reversal range between

Optimum strategies to elicit and maintain antibodies at mucosal portals of virus entry are critical for the development of vaccines against human immunodeficiency virus (HIV). Here we show in non-human primates that a novel regimen of repeated intravaginal delivery of a non-adjuvanted, soluble recombinant trimeric HIV-1CN54 clade C envelope glycoprotein (gp140) administered in Carbopol gel can prime for B-cell responses even in the absence of seroconversion. Following 3 cycles of repeated intravaginal administration, throughout each intermenses interval, 3 of 4 macaques produced or boosted systemic and mucosally-detected antibodies upon intramuscular immunisation with gp140 formulated in AS01 adjuvant. Reciprocally, a single intramuscular immunisation primed 3 of 4 macaques for antibody boosting after a single cycle of intravaginal immunisation. Virus neutralising activity was detected against clade C and clade B HIV-1 envelopes but was restricted to highly neutralisation sensitive pseudoviruses. PMID:21187177

The reaction between the bis(ethylene) complex [TpRh(C2 H4 )2 ], 1, (Tp=hydrotris(pyrazolyl)borate), and dimethyl acetylenedicarboxylate (DMAD) has been studied under different experimental conditions. A mixture of products was formed, in which TpRh(I) species were prevalent, whereas the presence of trapping agents, like water or acetonitrile, allowed for the stabilization and isolation of octahedral TpRh(III) compounds. An excess of DMAD gave rise to a small amount of the [2+2+2] cyclotrimerization product hexamethyl mellitate (6). Although no catalytic application of 1 was achieved, mechanistic insights shed light on the formation of stable rhodium species representing the resting state of the catalytic cycle of rhodium-mediated [2+2+2] cyclo(co)trimerization reactions. Metallacyclopentene intermediate species, generated from the activation of one alkyne and one ethylene molecule from 1, and metallacyclopentadiene species, formed by oxidative coupling of two alkynes to the rhodium centre, are crucial steps in the pathways leading to the final organometallic and organic products. PMID:27535720

Magnetization, 31P nuclear magnetic resonance study, and first-principles electronic structure calculations have been performed in the spin-1 trimer chain compound CaNi3(P2O7 )2. Two separate spectra arising from magnetically and crystallographically inequivalent P sites are observed. In the ordered state, the resonance lines for both the P sites (P1 and P2) are found to be split into two, which is clear microscopic evidence of the development of two-sublattice AFM order below TM. A nonnegligible contribution of ferromagnetic hyperfine field and dipolar field have also been seen in the ordered state. The first-principles calculations show that the intratrimer (J1) and intertrimer interactions (J2) are of weak ferromagnetic type with the values 2.85 and 1.49 meV, respectively, whereas the interchain interaction (J3) is of strong antiferromagnetic type with a value of 5.63 meV. The anisotropy of the imaginary part of dynamical spin susceptibility around TM along with the exponential decrement of 1 /T1 below TM indicate the probable participation of the Ni -3 d electron's orbital degrees of freedom in the ferrimagnetic transition. The dominance of orbital fluctuations over the spin fluctuations seems to be responsible for showing low value of the binding energy u of the local spin configuration (estimated from local spin models) and an unusually weak exponent in the power-law behavior of 1 /T1 below 50 K, in the paramagnetic state. Electronic structure calculations also reveal the importance of orbital degrees of freedom of Ni -3 d moments, which is consistent with our NMR data analysis.

Adult T cell leukemia (ATL) is a malignant lymphoproliferative disease caused by human T cell leukemia virus type I (HTLV-I). To develop an effective therapy against the disease, we have examined the oncolytic ability of an attenuated vaccinia virus (VV), LC16m8Δ (m8Δ), and an HTLV-I Tax-specific cytotoxic T lymphocyte (CTL) line, 4O1/C8, against an HTLV-I-infected rat T cell line, FPM1. Our results demonstrated that m8Δ was able to replicate in and lyse tumorigenic FPM1 cells but was incompetent to injure 4O1/C8 cells, suggesting the preferential cytolytic activity toward tumor cells. To further enhance the cytolysis of HTLV-I-infected cells, we modified m8Δ and obtained m8Δ/RT1AlSCTax180L, which can express a single chain trimer (SCT) of rat major histocompatibility complex class I with a Tax-epitope. Combined treatment with m8Δ/RT1AlSCTax180L and 4O1/C8 increased the cytolysis of FPM1V.EFGFP/8R cells, a CTL-resistant subclone of FPM1, compared with that using 4O1/C8 and m8Δ presenting an unrelated peptide, suggesting that the activation of 4O1/C8 by m8Δ/RT1AlSCTax180L further enhanced the killing of the tumorigenic HTLV-I-infected cells. Our results indicate that combined therapy of oncolytic VVs with SCTs and HTLV-I-specific CTLs may be effective for eradication of HTLV-I-infected cells, which evade from CTL lysis and potentially develop ATL. PMID:24791004

HOX proteins and some orphan homeodomain proteins form complexes with either PBX or MEIS subclasses of homeodomain proteins. This interaction can increase the binding specificity and transcriptional effectiveness of the HOX partner. Here we show that specific members of both PBX and MEIS subclasses form a multimeric complex with the pancreatic homeodomain protein PDX1 and switch the nature of its transcriptional activity. The two activities of PDX1 are exhibited through the 10-bp B element of the transcriptional enhancer of the pancreatic elastase I gene (ELA1). In pancreatic acinar cells the activity of the B element requires other elements of the ELA1 enhancer; in β-cells the B element can activate a promoter in the absence of other enhancer elements. In acinar cell lines the activity is mediated by a complex comprising PDX1, PBX1b, and MRG1 (MEIS2). In contrast, β-cell lines are devoid of PBX1b and MRG1, so that a trimeric complex does not form, and the β-cell-type activity is mediated by PDX1 without PBX1b and MRG1. The presence of specific nuclear isoforms of PBX and MEIS is precisely regulated in a cell-type-specific manner. The β-cell-type activity can be detected in acinar cells if the B element is altered to retain binding of PDX1 but prevent binding of the PDX1-PBX1b-MRG1 complex. These observations suggest that association with PBX and MEIS partners controls the nature of the transcriptional activity of the organ-specific PDX1 transcription factor in exocrine versus endocrine cells. PMID:9710595

The Ducreyi serum resistance A (DsrA) protein of Haemophilus ducreyi belongs to a large family of multifunctional outer membrane proteins termed trimeric autotransporter adhesins responsible for resistance to the bactericidal activity of human complement (serum resistance), agglutination and adhesion. The ability of DsrA to confer serum resistance and bind extracellular matrix proteins lies in its N-terminal passenger domain. We have previously reported that immunization with a recombinant form of the passenger domain of DsrA, rNT-DsrA, in complete/incomplete Freund's adjuvant, protects against a homologous challenge in swine. We present herein the results of an immunogenicity study in mice aimed at investigating the persistence, type of immune response, and the effect of immunization route and adjuvants on surrogates of protection. Our results indicate that a 20 μg dose of rNT-DsrA administered with alum elicited antisera with comparable bacterial surface reactivity to that obtained with complete/incomplete Freund's adjuvant. At that dose, high titers and bacterial surface reactivity persisted for 211 days after the first immunization. Administration of rNT-DsrA with CpG or imiquimod as adjuvants elicited a humoral response with similar quantity and quality of antibodies (Abs) as seen with Freund's adjuvant. Furthermore, intramuscular administration of rNT-DsrA elicited high-titer Abs with significantly higher reactivity to the bacterial surface than those obtained with subcutaneous immunization. All rNT-DsrA/adjuvant combinations tested, save CpG, elicited a Th2-type response. Taken together, these findings show that a 20 μg dose of rNT-DsrA administered with the adjuvants alum, CpG or imiquimod elicits high-quality Abs with reactivity to the bacterial surface that could protect against an H. ducreyi infection. PMID:26812077

The potency of CD8+ cytotoxic T lymphocyte (CTL) responses toward core antigen has been shown to affect the outcomes of hepatitis B virus (HBV) infection. Since single-chain trimers (SCT) composed of peptide epitope beta2-microglobulin (beta2m) and major histocompatibility complex (MHC) class I heavy chain covalently linked together in a single molecule have been shown to stimulate efficient CTL responses, we investigated the properties of human leucocyte antigen (HLA)-A2 SCTs encoding the HBV core antigen (HBcAg) epitopes C(18-27) and C(107-115). Transfection of NIH-3T3 cells with pcDNA3.0-SCT-C(18-27) and SCT-C(107-115) leads to stable presentation of HBcAg epitopes at the cell surface. HLA-A2.1/Kb transgenic mice vaccinated with the SCT constructs, either as a DNA vaccine alone or followed by a boost with recombinant vaccinia virus, were shown to generate HBcAg-specific CTL responses by enzyme-linked immunospot assay (ELISPOT) and in vitro interferon-gamma release experiments. HBcAg-specific CTLs from vaccinated HLA-A2.1/Kb transgenic mice were able to inhibit HBV surface and e antigen expression as indicated by HepG2.2.15 cells. Our data indicate that a DNA vaccine encoding a human HLA-A2 SCT with HBV epitopes can lead to stable, enhanced HBV core antigen presentation, and may be useful for the control of HBV infection in HLA-A2-positive HBV carriers. PMID:17244158

When plants are grown under stable light conditions their photosynthetic apparatus undergoes a long-term acclimation process. Acclimation to different light intensities involves changes in the organization and/or abundance of protein complexes in the thylakoid membranes. In this study, spinach plants were exposed to differing light intensities, and the structural organization of the major light-harvesting chlorophyll a/b-protein complex of photosystem II (LHCII) was investigated by analysing their trimeric subunits. Plants were exposed to three different light intensities, 100 μmol quanta m⁻² s⁻¹, 200 μmol quanta m⁻² s⁻¹ and an elevated light intensity, 400 μmol quanta m⁻² s⁻¹, sufficient to provoke a moderate stress response in the form of down regulation of PSII. "MicroRotofor" analysis showed the presence of LHCII with different pIs and revealed a clear decline in their abundance as light intensity increased from 100 to 400 μmol quanta m⁻² s⁻¹. The three subunits (Lhcb1, Lhcb2, Lhcb3) behaved differently from each other as: Lhcb1 decreased more significantly than Lhcb2, whereas Lhcb3 was reduced only at a light window at which Lhcb1 and Lhcb2 abundance has already been depleted under intense irradiation. Interestingly, we also found that isoforms of Lhcb1 subunit (Lhcb1.1; 1.2; 1.3) behaved differently in response to elevated light intensity, suggesting an essential role of these isoforms to light adaption and consequently explaining the presence of this multigenic family, often identified among higher plants. PMID:22099514

The reaction of N,N-bis(2-pyridylmethyl)-2-aminoethanol (bpaeOH), NaSCN/NaN(3), and metal (M) ions [M = Mn(II), Fe(II/III), Co(II)] in MeOH, leads to the isolation of a series of monomeric, trimeric, and tetrameric metal complexes, namely [Mn(bpaeOH)(NCS)(2)] (1), [Mn(bpaeO)(N(3))(2)] (2), [Fe(bpaeOH)(NCS)(2)] (3), [Fe(4)(bpaeO)(2)(CH(3)O)(2)(N(3))(8)] (4), [Co(bpaeOH)(NCS)(2)] (5), and [Co(3)(bpaeO)(2)(NO(3))(N(3))(4)](NO(3)) (6). These compounds have been investigated by single crystal X-ray diffractometry and magnetochemistry. In complex 1 the Mn(II) is bonded to one bpaeOH and two thiocyanate ions, while in complex 2 it is coordinated to a deprotonated bpaeO(-) and two azide ions. The oxidation states of manganese ions are 2+ for 1 and 3+ for 2, respectively, indicating that the different oxidation states depend on the type of binding anions. The structures of monomeric iron(II) and cobalt(II) complexes 3 and 5 with two thiocyanate ions are isomorphous to that of 1. Compounds 1, 2, 3, and 5 exhibit high-spin states in the temperature range 5 to 300 K. 4 contains two different iron(III) ions in an asymmetric unit, one is coordinated to a deprotonated bpaeO(-), an azide ion, and a methoxy group, and the other is bonded to three azide ions and two oxygens from bpaeO(-) and a methoxy group. Two independent iron(III) ions in 4 form a tetranuclear complex by symmetry. 4 displays both ferromagnetic and antiferromagnetic couplings (J = 9.8 and -14.3 cm(-1)) between the iron(III) ions. 6 is a mixed-valence trinuclear cobalt complex, which is formulated as Co(III)(S = 0)-Co(II)(S = 3/2)-Co(III)(S = 0). The effective magnetic moment at room temperature corresponds to the high-spin cobalt(II) ion (∼4.27 μ(B)). Interestingly, 6 showed efficient catalytic activities toward various olefins and alcohols with modest to excellent yields, and it has been proposed that a high-valent Co(V)-oxo species might be responsible for oxygen atom transfer in the olefin epoxidation and

Plant cell walls are a major source of dietary fiber. Hydroxycinnamates that are only minor components within the plant cell wall strongly influence the physico-chemical properties of the cell wall due to their ability to act as cross-links between polysaccharides with each other, to lignin, and to ...

Density functional theory is used to model a series of cyclic phosphazenes, with and without coordinated Li+. Two pendant groups are used, ethoxy and 2,2,2-trifluoroethoxy, in varying combinations to generate phosphazenes with 0, 1, 2, 3, or 6 trifluoro groups. In all cases, Li+ sits in a pocket on the ring, always bonding to a ring nitrogen, and can be three- or four-coordinate, depending on the local environment. Three-coordinate occurs when no fluorines are close enough to interact, with the lithium bonding to a ring nitrogen and the two adjacent oxygens. When Li+ is four-coordinate, the bonding varies between the ring nitrogen, two adjacent oxygens, and one fluorine, or the ring nitrogen, one adjacent oxygen, and two fluorines. All of the possible symmetry unique structures have been calculated. The binding strength of Li+ steadily decreases, from 74.93 kcal/mol with no trifluoro groups, to 58.01 kcal/mol when 6 trifluoro groups are present. The decrease is attributed to the electron withdrawing effect of the trifluoro groups, and also to distortions in the geometry to accommodate Li-F interactions.

The Oca family is a novel class of autotransporter-adhesins with highest structural similarity in their C-terminal transmembrane region, which supposedly builds a beta-barrel pore in the outer membrane (OM). The prototype of the Oca family is YadA, an adhesin of Yersinia enterocolitica and Yersinia pseudotuberculosis. YadA forms a homotrimeric lollipop-like structure on the bacterial surface. The C-terminal regions of three YadA monomers form a barrel in the OM and translocate the trimeric N-terminal passenger domain, consisting of stalk, neck, and head region to the exterior. To elucidate the structural and functional role of the C-terminal translocator domain (TLD) and to assess its promiscuous capability with respect to transport of related passenger domains, we constructed chimeric YadA proteins, which consist of the N-terminal YadA passenger domain and C-terminal TLDs of Oca family members UspA1 (Moraxella catarrhalis), EibA (Escherichia coli), and Hia (Haemophilus influenzae). These constructs were expressed in Y. enterocolitica and compared for OM localization, surface exposure, oligomerization, adhesion properties, serum resistance, and mouse virulence. We demonstrate that all chimeric YadA proteins translocated the YadA passenger domain across the OM. Y. enterocolitica strains producing YadA chimeras or wild-type YadA showed comparable binding to collagen and epithelial cells. However, strains producing YadA chimeras were attenuated in serum resistance and mouse virulence. These results demonstrate for the first time that TLDs of Oca proteins of different origin are efficient translocators of the YadA passenger domain and that the cognate TLD of YadA is essential for bacterial survival in human serum and mouse virulence. PMID:18487327

A new class of rigid twisted truxenone oligomers with an enlarged π backbone has been established by oxidative dimerization reactions. The resulting extended conjugated systems have large extinction coefficients and low-lying LUMO levels and show good solubility in common organic solvents, thus making them attractive compounds as new electron acceptors in organic electronics. Their suitability as electron acceptors has been demonstrated in bulk-heterojunction organic solar cells with poly({4,8-bis[(2-ethylhexyl)oxy]benzo[1,2-b:4,5-b']dithiophene-2,6-diyl}{3-fluoro-2-[(2-ethylhexyl)carbonyl]thieno[3,4-b]thiophenediyl}) (PTB7) as the donor material. PMID:26891096

For the simplest cationic argon cluster, Ar{sub 3}{sup +}, the topographical characteristics of the ground-state potential energy surface (PES), the mode coupling and the claswsical intramolecular dynamics are studied; PES data have been obtained by the diatomics-in-molecules approach of Kuntz et al. The results show that Ar{sub 3}{sup +} s a rather floppy system with rapid vibrational energy redistribution and early onset of classical chaos.

Plant cell walls are a major source of dietary fiber. Although hydroxycinnamates are only minor components within the plant cell wall, they strongly influence the physico-chemical properties of the cell wall due to their ability to act as cross-links between polysaccharides with each other, to ligni...

We present results of ring polymer molecular dynamics simulations that shed light on the effects of nuclear quantum fluctuations on tunneling motions in cyclic [H2O]3 and [D2O]3, at the representative temperature of T = 75 K. In particular, we focus attention on free energies associated with two key isomerization processes: The first one corresponds to flipping transitions of dangling OH bonds, between up and down positions with respect to the O-O-O plane of the cluster; the second involves the interchange between connecting and dangling hydrogen bond character of the H-atoms in a tagged water molecule. Zero point energy and tunneling effects lead to sensible reductions of the free energy barriers. Due to the lighter nature of the H nuclei, these modifications are more marked in [H2O]3 than in [D2O]3. Estimates of the characteristic time scales describing the flipping transitions are consistent with those predicted based on standard transition-state-approximation arguments.

The HIV-1 envelope glycoprotein spike is the target of neutralizing antibody attack, and hence represents the only relevant viral antigen for antibody-based vaccine design. Various approaches have been attempted to recapitulate Env in membrane-anchored and soluble forms, and these will be discussed here in the context of recent successes and challenges still to be overcome. PMID:26344344

We present results of ring polymer molecular dynamics simulations that shed light on the effects of nuclear quantum fluctuations on tunneling motions in cyclic [H2O]3 and [D2O]3, at the representative temperature of T = 75 K. In particular, we focus attention on free energies associated with two key isomerization processes: The first one corresponds to flipping transitions of dangling OH bonds, between up and down positions with respect to the O-O-O plane of the cluster; the second involves the interchange between connecting and dangling hydrogen bond character of the H-atoms in a tagged water molecule. Zero point energy and tunneling effects lead to sensible reductions of the free energy barriers. Due to the lighter nature of the H nuclei, these modifications are more marked in [H2O]3 than in [D2O]3. Estimates of the characteristic time scales describing the flipping transitions are consistent with those predicted based on standard transition-state-approximation arguments. PMID:26874474

The photoabsorption spectrum of He_3^+ is calculated for two semiempirical models of intracluster interactions and compared with available experimental data reported in the middle UV range [H. Haberland and B. von Issendorff, J. Chem. Phys. 102, 8773 (1995)]. Nuclear delocalization effects are investigated via several approaches comprising quantum samplings using either exact or approximate (harmonic) nuclear wavefunctions, as well as classical samplings based on the Monte Carlo methodology. Good agreement with the experiment is achieved for the model by Knowles et al., [Mol. Phys. 85, 243 (1995); Knowles et al., Mol. Phys. 87, 827 (1996)] whereas the model by Calvo et al., [J. Chem. Phys. 135, 124308 (2011)] exhibits non-negligible deviations from the experiment. Predictions of far UV absorption spectrum of He_3^+, for which no experimental data are presently available, are reported for both models and compared to each other as well as to the photoabsorption spectrum of He_2^+. A simple semiempirical point-charge approximation for calculating transition probabilities is shown to perform well for He_3^+.

The photoabsorption spectrum of He3(+) is calculated for two semiempirical models of intracluster interactions and compared with available experimental data reported in the middle UV range [H. Haberland and B. von Issendorff, J. Chem. Phys. 102, 8773 (1995)]. Nuclear delocalization effects are investigated via several approaches comprising quantum samplings using either exact or approximate (harmonic) nuclear wavefunctions, as well as classical samplings based on the Monte Carlo methodology. Good agreement with the experiment is achieved for the model by Knowles et al., [Mol. Phys. 85, 243 (1995); Mol. Phys. 87, 827 (1996)] whereas the model by Calvo et al., [J. Chem. Phys. 135, 124308 (2011)] exhibits non-negligible deviations from the experiment. Predictions of far UV absorption spectrum of He3(+), for which no experimental data are presently available, are reported for both models and compared to each other as well as to the photoabsorption spectrum of He2(+). A simple semiempirical point-charge approximation for calculating transition probabilities is shown to perform well for He3(+). PMID:24289357

The photoabsorption spectrum of He{sub 3}{sup +} is calculated for two semiempirical models of intracluster interactions and compared with available experimental data reported in the middle UV range [H. Haberland and B. von Issendorff, J. Chem. Phys. 102, 8773 (1995)]. Nuclear delocalization effects are investigated via several approaches comprising quantum samplings using either exact or approximate (harmonic) nuclear wavefunctions, as well as classical samplings based on the Monte Carlo methodology. Good agreement with the experiment is achieved for the model by Knowles et al., [Mol. Phys. 85, 243 (1995); Mol. Phys. 87, 827 (1996)] whereas the model by Calvo et al., [J. Chem. Phys. 135, 124308 (2011)] exhibits non-negligible deviations from the experiment. Predictions of far UV absorption spectrum of He{sub 3}{sup +}, for which no experimental data are presently available, are reported for both models and compared to each other as well as to the photoabsorption spectrum of He{sub 2}{sup +}. A simple semiempirical point-charge approximation for calculating transition probabilities is shown to perform well for He{sub 3}{sup +}.

Ultra-fast Energy Transfer from Monomer to Dimer within a Trimeric Molecule New Progress in Heterogeneous Catalysis Research Key Progress in Research on Terrestrial Carbon Cycle in China A New Progress in Research on the Mechanism of Bio-Invasion New Findings in Anti-viral infection and Control of Inflammation Major Headway in Avian Origin Research New Progress in Gold-Nanoparticle-Based Biochips Topological Insulator Research Made Important Progress Major Progress in Biodiversity Achieved New Developments of Direct Methods in Protein Crystallography Major Progress in China-UK Collaboration on the Causal Relationship between Volcanic Activity and Biological Distinction News in Brief: NSFC set up "Research Fund for Young Foreign Scholars" How Often Does Human DNA Mutate? Research Progress on Colossal Anisotropic Magneto Resistive Effect

MicroProteins are short, single domain proteins that act by sequestering larger, multi-domain proteins into non-functional complexes. MicroProteins have been identified in plants and animals, where they are mostly involved in the regulation of developmental processes. Here we show that two Arabidopsis thaliana microProteins, miP1a and miP1b, physically interact with CONSTANS (CO) a potent regulator of flowering time. The miP1a/b-type microProteins evolved in dicotyledonous plants and have an additional carboxy-terminal PF(V/L)FL motif. This motif enables miP1a/b microProteins to interact with TOPLESS/TOPLESS-RELATED (TPL/TPR) proteins. Interaction of CO with miP1a/b/TPL causes late flowering due to a failure in the induction of FLOWERING LOCUS T (FT) expression under inductive long day conditions. Both miP1a and miP1b are expressed in vascular tissue, where CO and FT are active. Genetically, miP1a/b act upstream of CO thus our findings unravel a novel layer of flowering time regulation via microProtein-inhibition. PMID:27015278

There is widespread agreement that the clamp loader of the Escherichia coli replicase has the composition DnaX3δδ'χψ. Two DnaX proteins exist in E. coli, full length τ and a truncated γ that is created by ribosomal frameshifting. τ binds DNA polymerase III tightly; γ does not. There is a controversy as to whether or not DNA polymerase III holoenzyme (Pol III HE) contains γ. A three-τ form of Pol III HE would contain three Pol IIIs. Proponents of the three-τ hypothesis have claimed that γ found in Pol III HE might be a proteolysis product of τ. To resolve this controversy, we constructed a strain that expressed only τ from a mutated chromosomal dnaX. γ containing a C-terminal biotinylation tag (γ-Ctag) was provided in trans at physiological levels from a plasmid. A 2000-fold purification of Pol III* (all Pol III HE subunits except β) from this strain contained one molecule of γ-Ctag per Pol III* assembly, indicating that the dominant form of Pol III* in cells is Pol III2τ2 γδδ'χψ. Revealing a role for γ in cells, mutants that express only τ display sensitivity to ultraviolet light and reduction in DNA Pol IV-dependent mutagenesis associated with double-strand-break repair, and impaired maintenance of an F' episome. PMID:26786318

The results of ab-initio calculations are reported for (1) small transition metal clusters and (2) potential energy surfaces for chemical reactions important in hydrogen combustion and high temperature air chemistry.

There is widespread agreement that the clamp loader of the Escherichia coli replicase has the composition DnaX3δδ’χψ. Two DnaX proteins exist in E. coli, full length τ and a truncated γ that is created by ribosomal frameshifting. τ binds DNA polymerase III tightly; γ does not. There is a controversy as to whether or not DNA polymerase III holoenzyme (Pol III HE) contains γ. A three-τ form of Pol III HE would contain three Pol IIIs. Proponents of the three-τ hypothesis have claimed that γ found in Pol III HE might be a proteolysis product of τ. To resolve this controversy, we constructed a strain that expressed only τ from a mutated chromosomal dnaX. γ containing a C-terminal biotinylation tag (γ-Ctag) was provided in trans at physiological levels from a plasmid. A 2000-fold purification of Pol III* (all Pol III HE subunits except β) from this strain contained one molecule of γ-Ctag per Pol III* assembly, indicating that the dominant form of Pol III* in cells is Pol III2τ2 γδδ’χψ. Revealing a role for γ in cells, mutants that express only τ display sensitivity to ultraviolet light and reduction in DNA Pol IV-dependent mutagenesis associated with double-strand-break repair, and impaired maintenance of an F’ episome. PMID:26786318

MicroProteins are short, single domain proteins that act by sequestering larger, multi-domain proteins into non-functional complexes. MicroProteins have been identified in plants and animals, where they are mostly involved in the regulation of developmental processes. Here we show that two Arabidopsis thaliana microProteins, miP1a and miP1b, physically interact with CONSTANS (CO) a potent regulator of flowering time. The miP1a/b-type microProteins evolved in dicotyledonous plants and have an additional carboxy-terminal PF(V/L)FL motif. This motif enables miP1a/b microProteins to interact with TOPLESS/TOPLESS-RELATED (TPL/TPR) proteins. Interaction of CO with miP1a/b/TPL causes late flowering due to a failure in the induction of FLOWERING LOCUS T (FT) expression under inductive long day conditions. Both miP1a and miP1b are expressed in vascular tissue, where CO and FT are active. Genetically, miP1a/b act upstream of CO thus our findings unravel a novel layer of flowering time regulation via microProtein-inhibition. PMID:27015278

Estolides are a class of esters based on vegetable oils that are formed when the carboxylic acid functionality of one fatty acid reacts at the site of unsaturation of another fatty acid to form an ester linkage. The objective of this preliminary study was to separate coco-oleic estolide into two com...

CASSCF/CCI calculations are presented for the low-lying states of Y3. Comparison of the wave functions for Y3 and Sc3 indicates substantial 4d-5p hybridization in Y3, but little 3d-4p hybridization in Sc3. The increased 4d-5p hybridization leads to stabilization of 4dpi bonding with respect to 4dsigma bonding for equilateral triangle Y3, and also leads to 4d-5p bonding for linear geometries. These effects lead to a different ordering of states for equilateral triangle geometries and a smaller excitation energy to the linear configuration for Y3 as compared to Sc3.

During retrovirus particle maturation, the assembled Gag polyprotein is cleaved by the viral protease into matrix (MA), capsid (CA), and nucleocapsid (NC) proteins. To form the mature viral capsid, CA rearranges, resulting in a lattice composed of hexameric and pentameric CA units. Recent structural studies of assembled HIV-1 CA revealed several inter-subunit interfaces in the capsid lattice, including a three-fold interhexamer interface that is critical for proper capsid stability. Although a general architecture of immature particles has been provided by cryo-electron tomographic studies, the structural details of the immature particle and the maturation pathway remain unknown. Here, we used cryo-electron microscopy (cryoEM) to determine the structure of tubular assemblies of the HIV-1 CA-SP1-NC protein. Relative to the mature assembled CA structure, we observed a marked conformational difference in the position of the CA-CTD relative to the NTD in the CA-SP1-NC assembly, involving the flexible hinge connecting the two domains. This difference was verified via engineered disulfide crosslinking, revealing that inter-hexamer contacts, in particular those at the pseudo three-fold axis, are altered in the CA-SP1-NC assemblies compared to the CA assemblies. Results from crosslinking analyses of mature and immature HIV-1 particles containing the same Cys substitutions in the Gag protein are consistent with these findings. We further show that cleavage of preassembled CA-SP1-NC by HIV-1 protease in vitro leads to release of SP1 and NC without disassembly of the lattice. Collectively, our results indicate that the proteolytic cleavage of Gag leads to a structural reorganization of the polypeptide and creates the three-fold interhexamer interface, important for the formation of infectious HIV-1 particles. PMID:22927821

The calculation of potential energy surfaces for chemical reactions was the focus of investigation. Two groups of reactions were considered: the subset of reactions important in H2 combustion, and high temperature air chemistry reactions (O + N yields NO + N and N + O2 yields NO + O).

The present study describes the designed synthesis, X-ray structures, and magnetic properties of two 2D cyanobridged heterobimetallic W(V)-Co(II) networks, {[W(CN)8]2[Co(phpy)4]3}·2CH3OH·2H2O (1) and {[W(CN)8]2[Co(4-spy)4]3}·6H2O (2) (phpy = 4-phenylpyridine, 4-spy = 4-styrylpyridine). Both compounds consist of cyano-bridged 12-metal 36-membered ring units, Co6W6(CN)12, joined by organic linkers into a 2D plane. The layer presents a corrugated configuration in compound 1 and a plane configuration in compound 2 due to different π-π stacking interactions. Magnetic measurements reveal that both 1 and 2 have a transition to the spin glass-like phase due to competitive magnetic interactions. PMID:26076432

We experimentally studied the dissociation dynamics of a highly charged Ar3 cluster initiated by a high-energy electron. The dissociation patterns of the correlated ions from a two-body and a three-body Coulombic explosion (CE) of (Ar3)2+ suggest that predissociation alters the evolution of radiative charge transfer. The three-body CE in (Ar3)4+ and (Ar3)5+ is driven, after double ionization of one constituent Ar atom, by single ionization with a simultaneous interatomic Coulombic decay process.

Glycosylation-inhibiting factor (GIF) is a cytokine that is involved in the regulation of IgE synthesis. The crystal structure of recombinant human GIF was determined by the multiple isomorphous replacement method. The structure was refined to an R factor of 0.168 at 1.9 angstrom resolution. The overall structure is seen to consist of three interconnected subunits forming a barrel with three 6-stranded beta-sheets on the inside and six alpha-helices on the outside. There is a 5-angstrom-diameter "hole" through the middle of the barrel. The barrel structure of GIF in part resembles other "trefoil" cytokines such as interleukin 1 and fibroblast growth factor. Each subunit has a new class of alpha + beta sandwich structure consisting of two beta-alpha-beta motifs. These beta-alpha-beta motifs are related by a pseudo-twofold axis and resemble both interleukin 8 and the peptide binding domain of major histocompatibility complex protein, although the topology of the polypeptide chain is quite different. Images Fig. 1 Fig. 3 PMID:8610159

Glycosylation-inhibiting factor (GIF) is a cytokine that is involved in the regulation of IgE synthesis. The crystal structure of recombinant human GIF was determined by the multiple isomorphous replacement method. The structure was refined to an R factor of 0.168 at 1.9 angstrom resolution. The overall structure is seen to consist of three interconnected subunits forming a barrel with three 6-stranded beta-sheets on the inside and six alpha-helices on the outside. There is a 5-angstrom-diameter "hole" through the middle of the barrel. The barrel structure of GIF in part resembles other "trefoil" cytokines such as interleukin 1 and fibroblast growth factor. Each subunit has a new class of alpha + beta sandwich structure consisting of two beta-alpha-beta motifs. These beta-alpha-beta motifs are related by a pseudo-twofold axis and resemble both interleukin 8 and the peptide binding domain of major histocompatibility complex protein, although the topology of the polypeptide chain is quite different. PMID:8610159

Background The COOH terminal peptide of Pro-collagen type I (PICP, also called C3) is chemotactic for endothelial melanoma and breast cancer cells. PICP induces the expression of Metalloproteinases-2 and -9, of Vascular endothelial growth factor and of the chemokine CXCL-12 receptor CXCR4 in MDA MB231 breast carcinoma cells in vitro. Methods We used a model of xenografts in BalbC/nude mice obtaining tumors by implanting in contro-lateral subcutaneous positions MDA MB231 cells added or not with purified PICP and studied the earlier phases of tumor development, up to 48 days from implant, by histology, immunostain and in situ hybridization. Results Addition of PICP promotes rapid vascularization of the tumors while does not affect mitotic and apoptotic indexes and overall tumor growth. PICP-treated, relative to control tumors, show up-modulation of Vascular endothelial factor, Metalloproteinase-9 and CXCR4, all tumor prognostic genes; they also show down-modulation of the endogenous Metalloproteinase inhibitor, reversion-inducing-cysteine-rich protein with kazal motifs, and a different pattern of modulation of Tissue Inhibitor of Metalloproteinase-2. These changes occur in absence of detectable expression of CXCL-12, up to 38 days, in control and treated tumors. Conclusion PICP has an early promoting effect in the acquisition by the tumors of prometastatic phenotype. PICP may be play a relevant role in the productive interactions between stroma and tumor cells by predisposing the tumor cells to respond to the proliferation stimuli ensuing the activation of signaling by engagement of CXCR4 by cytokines and by fostering their extravasion, due to the induction of increased vascular development. PMID:19226458

Reactions of the trinuclear Lewis acid perfluoro-ortho-phenylene)mercury [(o-HgC6F4)3] (1) with the polypnictogen complex [CpMo(CO)2(η(3)-P3)] (2) containing a cyclo-P3 ligand and the series of E2 complexes [{CpMo(CO)2}2(μ,η(2):η(2)-E2)] (E = P(3a), As(3b), Sb(3c), Bi(3d)) are reported. In all cases, the reaction products show very weak interactions between the En ligand complexes and the Lewis acid 1, as evidenced by their highly dynamic behaviour in solution and the formation of adducts in the solid state showing HgE contacts below the respective sum of the van der Waals radii. The complexes 2 (P3), 3a (P2) and 3b (As2) show interactions of only one pnictogen atom with all three Hg atoms of 1. The complex 3c (Sb2) forms two adducts with 1 showing either a side-on coordination of the Sb2 dumbbell towards Hg or an end-on coordination of both Sb atoms towards two independent molecules of 1. The Bi2 complex 3d shows an almost parallel alignment of the Bi2 dumbbell situated above the center of the planar Lewis acid 1. The arrangements of the E2 complex series towards 1 are rationalized with the help of electrostatic potential maps obtained by DFT calculations. Finally the structural characterizations of a new modification of the free Sb2 complex 3c, the Bi2 complex 3d, the starting material of its preparation [Bi{CpMo(CO)3}3] (4) and an unprecedented 'Cr4As5' cluster 5 are presented. PMID:27461890

Background DNA vaccines remain an important component of HIV vaccination strategies, typically as part of a prime/boost vaccination strategy with viral vector or protein boost. A number of DNA prime/viral vector boost vaccines are currently being evaluated for both preclinical studies and in Phase I and Phase II clinical trials. These vaccines would benefit from molecular adjuvants that increase correlates of immunity during the DNA prime. While HIV vaccine immune correlates are still not well defined, there are a number of immune assays that have been shown to correlate with protection from viral challenge including CD8+ T cell avidity, antigen-specific proliferation, and polyfunctional cytokine secretion. Methodology and Principal Findings Recombinant DNA vaccine adjuvants composed of a fusion between Surfactant Protein D (SP-D) and either CD40 Ligand (CD40L) or GITR Ligand (GITRL) were previously shown to enhance HIV-1 Gag DNA vaccines. Here we show that similar fusion constructs composed of the TNF superfamily ligands (TNFSFL) 4-1BBL, OX40L, RANKL, LIGHT, CD70, and BAFF can also enhanced immune responses to a HIV-1 Gag DNA vaccine. BALB/c mice were vaccinated intramuscularly with plasmids expressing secreted Gag and SP-D-TNFSFL fusions. Initially, mice were analyzed 2 weeks or 7 weeks following vaccination to evaluate the relative efficacy of each SP-D-TNFSFL construct. All SP-D-TNFSFL constructs enhanced at least one Gag-specific immune response compared to the parent vaccine. Importantly, the constructs SP-D-4-1BBL, SP-D-OX40L, and SP-D-LIGHT enhanced CD8+ T cell avidity and CD8+/CD4+ T cell proliferation 7 weeks post vaccination. These avidity and proliferation data suggest that 4-1BBL, OX40L, and LIGHT fusion constructs may be particularly effective as vaccine adjuvants. Constructs SP-D-OX40L, SP-D-LIGHT, and SP-D-BAFF enhanced Gag-specific IL-2 secretion in memory T cells, suggesting these adjuvants can increase the number of self-renewing Gag-specific CD8+ and/or CD4+ T cells. Finally adjuvants SP-D-OX40L and SP-D-CD70 increased TH1 (IgG2a) but not TH2 (IgG1) antibody responses in the vaccinated animals. Surprisingly, the B cell-activating protein BAFF did not enhance anti-Gag antibody responses when given as an SP-D fusion adjuvant, but nonetheless enhanced CD4+ and CD8+ T cell responses. Conclusions We present evidence that various SP-D-TNFSFL fusion constructs can enhance immune responses following DNA vaccination with HIV-1 Gag expression plasmid. These data support the continued evaluation of SP-D-TNFSFL fusion proteins as molecular adjuvants for DNA and/or viral vector vaccines. Constructs of particular interest included SP-D-OX40L, SP-D-4-1BBL, SP-D-LIGHT, and SP-D-CD70. SP-D-BAFF was surprisingly effective at enhancing T cell responses, despite its inability to enhance anti-Gag antibody secretion. PMID:22146759

A number of ruthenium complexes were tested for their ability to induce filamentation in Escherichia coli. These included monomeric and dimeric complexes with ruthenium in the II or III oxidation states, as well as mixed-valence complexes with ruthenium in the (II,III) oxidation states. In general, dimeric mixed-valence Ru(II,III) complexes were the most active class of compound, although some complexes of this type were relatively inactive. These were pyrazine- or bipyridyl-bridged complexes which are known to involve strong metal-ligand interaction, which stabilizes the Ru(II) oxidation state. Some Ru(III) complexes were also significantly active in induction of filamentous growth in E. coli. One of these was [Ru(NH3)5Cl]Cl2, which did not inhibit electron transport, Mg2+-ATPase activity or DNA synthesis in E. coli, but like [Ru2(NH3)6Br3]Br2 X H2O was a potent inhibitor of respiration-driven calcium transport in the organism. Filament-inducing activity of the complex was reduced in the presence of NaCl, but not in the presence of added Ca2+, ethanol, calcium pantothenate, or E. coli 'division promoting extract'. This behaviour is also similar to that of [Ru2(NH3)6Br3]Br2 X H2O. It is suggested that both complexes may induce filamentation in E. coli by a common mechanism, which may involve interference with calcium metabolism, or a wall or membrane target, rather than interaction with DNA. PMID:3159489

Kohn-Sham density functional theory (KS-DFT) calculations were performed for the association complexes Cun-L, with n=1, 2, 3 and L=NH3, CO, and C2H4. Two geometries for Cu2-L are considered; with the ligand bonded to a single copper atom (``atop,'' or A), and with the ligand bonded to both atoms (``bridge,'' or B). In addition to A and B, a third geometry was considered for Cu3-L, with the ligand bonded to all three copper atoms; in each case, no minimum was found for that third geometry. I report fully optimized equilibrium geometries and harmonic frequencies calculated within the local spin density (LSD) approximation for all the bound complexes and estimates of their binding energies obtained with a gradient-corrected exchange-correlation functional. Structure A is the most stable in all cases but, for Cu3CO and Cu3C2H4, structure B is only a few kcal/mol higher in energy. The energetic contribution from the geometrical relaxation of Cu3 ranges from essentially zero (Cu3NH3 B) to 3.4 kcal/mol (Cu3CO B). In agreement with previous calculations on Cun-C2H2 and with experiments, the calculated Cun-L binding energy is found to increase with n for all ligands. Although the bonding mechanism differs among the three ligands, repulsion of a filled ligand orbital with the half-filled 4s orbital of copper (or 4s-derived molecular orbitals of Cu2 and Cu3) always plays an important role and is responsible for the smaller binding energies in the CuL complexes. This repulsion decreases from Cu to Cu2 because of charge accumulation in Cu-Cu midbond region and of the greater polarizability of Cu2. The Cu3L binding energies are larger than those of Cu2L mostly because of the greater involvement of copper 4p orbitals in bonding to the ligand. The ligand vibrational frequency shifts relative to the free molecules are compared to experiment and discussed in relation to the nature of the metal-ligand interaction. In particular, an interesting correlation, between the frequency of the NH3 umbrella mode and the metal-NH3 binding energy, is likely due to the electrostatic nature of the bond.

The molecular structure of both the neutral and negatively charged diatomic and triatomic systems containing the Cu, Ag, and Au metals are determined from ab initio calculations. For the neutral triatomic systems, the lowest energy structure is found to be triangular. The relative stability of the 2A1 and 2B2 structures can be predicted simply by knowing the constituent diatomic bond distances and atomic electron affinities (EAs). The lowest energy structure is linear for all of the negative ions. For anionic clusters containing Au, the Au atom(s) preferentially occupy the terminal position(s). The EAs of the heteronuclear systems can be predicted relatively accurately from a weighted average of the corresponding homonuclear systems. Although the theoretical EAs are systematically too small, accurate predictions for the EAs of the triatomics are obtained by uniformly scaling the ab initio results using the accurate experimental EA values available for the atoms and homonuclear diatomics.

Picosecond time-resolved polarized fluorescence experiments involving time-correlated single-photon counting have studied rotational coherence phenomena of hydrogen-bonded and other molecular aggregates in their lowest excited singlet states. The experiments are supported by detailed simulations. Using the molecule 2,5-diphenyl-1,3,4-oxadiazole (PPD) as a host species, experiments have compared van der Waals aggregates with Ar1,2, (CH4)1,2, (H2O)1,2, (CH3OH)1,2, (C2H5OH)1, and (1-C3H7OH)1. Bare PPD, and the argon and methane aggregates all exhibit prominent J-type recurrences. The resulting sums of rotational constants (B+C) are consistent with center-of-mass-bound, three-dimensional structures, having out-of-plane distances for the attached species of 3.3-3.5 Å. The 1:2 aggregates involving argon and methane exhibit additive spectral shifts and nearly additive rotational recurrence times. This shows that the sites for addition of consecutive species are equivalent. Calculations of rotational constants confirm these findings. All except the Ar 1:2 cluster exist close to the prolate symmetric top limit. On the other hand, the excitation spectra of complexes involving hydrogen-bonding species all show small complexation shifts at the 1:1 level and disproportionately larger shifts at the 1:2 level. Similar nonadditive behavior is seen for the rotational recurrence transients. Hydrogen-bonded species differ from the nonpolar cases, since they show both prominent C-type and J-type transients. This shows that these species all differ significantly from prolate symmetric tops. Detailed simulations reveal that all of the hydrogen-bonding species produce aggregates that involve a single hydrogen bond to one of the PPD nitrogen atoms. This imposes a planar type of structure on the 1:1 water and methanol complexes. On the other hand, the aggregates methanol 1:2, ethanol 1:1, and propanol 1:1 all involve a distinct out-of-plane twist, consistent with the increasing influence of dispersive interactions. Hydrogen bond distances (N...H-O) are found to be in the range 2.7-2.9 Å, and the hydrogen-bond angles (N-N...H-O), relative to the PPD long axis, range from 115° to 130°. In addition, the water and methanol 1:2 aggregates both contain hydrogen-bonded dimer units that resemble the free dimers of each species as identified by infrared and microwave techniques. For example, we find the (O...H-O) distance in the methanol dimer complex to be ≊2.7 Å.

The DEAD-box RNA helicase Ded1, which is essential in yeast and known as DDX3 in humans, shuttles between the nucleus and cytoplasm and takes part in several basic processes including RNA processing and translation. A key interacting partner of Ded1 is the exportin Xpo1, which together with the GTP-bound state of the small GTPase Ran, facilitates unidirectional transport of Ded1 out of the nucleus. Here we demonstrate that Xpo1 and Ran[GTP] together reduce the RNA-stimulated ATPase and helicase activities of Ded1. Binding and inhibition of Ded1 by Xpo1 depend on the affinity of the Ded1 nuclear export sequence (NES) for Xpo1 and the presence of Ran[GTP]. Association with Xpo1/Ran[GTP] reduces RNA-stimulated ATPase activity of Ded1 by increasing the apparent KM for the RNA substrate. Despite the increased KM, the Ded1:Xpo1:Ran[GTP] ternary complex retains the ability to bind single stranded RNA, suggesting that Xpo1/Ran[GTP] may modulate the substrate specificity of Ded1. These results demonstrate that, in addition to transport, exportins such as Xpo1 also have the capability to alter enzymatic activities of their cargo. PMID:26120835

Recent X-ray crystallographic studies of Pol II in complex with the general transcription factor (GTF) IIB have begun to provide insights into the mechanism of transcription initiation. These structures have also shed light on the architecture of the transcription preinitiation complex (PIC). However, structural characterization of a functional PIC is still lacking, and even the topological arrangement of the GTFs in the Pol II complex is a matter of contention. We have extended our activity-based affinity crosslinking studies, initially developed to investigate the interaction of bacterial RNA polymerase with σ, to the eukaryotic transcription machinery. Towards that end, we sought to identify GTFs that are within the Pol II active site in a functioning PIC. We provide biochemical evidence that TFIIB is located within ∼9 Å of the -2 site of promoter DNA, where it is positioned to play a role in de novo transcription initiation. PMID:25774659

Leafy spurge is a deep rooted perennial weed that propagates both by seeds and underground adventitious buds located on the crown and roots (crown and root buds). As buds develop during the normal growing season, they are maintained in a quiescent state through correlative inhibition. To enhance our...

Recent X-ray crystallographic studies of Pol II in complex with the general transcription factor (GTF) IIB have begun to provide insights into the mechanism of transcription initiation. These structures have also shed light on the architecture of the transcription preinitiation complex (PIC). However, structural characterization of a functional PIC is still lacking, and even the topological arrangement of the GTFs in the Pol II complex is a matter of contention. We have extended our activity-based affinity crosslinking studies, initially developed to investigate the interaction of bacterial RNA polymerase with σ, to the eukaryotic transcription machinery. Towards that end, we sought to identify GTFs that are within the Pol II active site in a functioning PIC. We provide biochemical evidence that TFIIB is located within ∼9 Å of the −2 site of promoter DNA, where it is positioned to play a role in de novo transcription initiation. PMID:25774659

Clonorchiasis, which is induced by the infection of Clonorchis sinensis (C. sinensis), is highly associated with cholangiocarcinoma. Because the available examination, treatment and interrupting transmission provide limited opportunities to prevent infection, it is urgent to develop integrated strategies to prevent and control clonorchiasis. Glycolytic enzymes are crucial molecules for trematode survival and have been targeted for drug development. Hexokinase of C. sinensis (CsHK), the first key regulatory enzyme of the glycolytic pathway, was characterized in this study. The calculated molecular mass (Mr) of CsHK was 50.0 kDa. The obtained recombinant CsHK (rCsHK) was a homotrimer with an Mr of approximately 164 kDa, as determined using native PAGE and gel filtration. The highest activity was obtained with 50 mM glycine-NaOH at pH 10 and 100 mM Tris-HCl at pH 8.5 and 10. The kinetics of rCsHK has a moderate thermal stability. Compared to that of the corresponding negative control, the enzymatic activity was significantly inhibited by praziquantel (PZQ) and anti-rCsHK serum. rCsHK was homotropically and allosterically activated by its substrates, including glucose, mannose, fructose, and ATP. ADP exhibited mixed allosteric effect on rCsHK with respect to ATP, while inorganic pyrophosphate (PPi) displayed net allosteric activation with various allosteric systems. Fructose behaved as a dose-dependent V activator with the substrate glucose. Glucose-6-phosphate (G6P) displayed net allosteric inhibition on rCsHK with respect to ATP or glucose with various allosteric systems in a dose-independent manner. There were differences in both mRNA and protein levels of CsHK among the life stages of adult worm, metacercaria, excysted metacercaria and egg of C. sinensis, suggesting different energy requirements during different development stages. Our study furthers the understanding of the biological functions of CsHK and supports the need to screen for small molecule inhibitors of CsHK to interfere with glycolysis in C. sinensis. PMID:25232723

The electronic structure and magnetic moments of free Mn{sub 2}{sup +} and Mn{sub 3}{sup +} are characterized by 2p x-ray absorption and x-ray magnetic circular dichroism spectroscopy in a cryogenic ion trap that is coupled to a synchrotron radiation beamline. Our results directly show that localized magnetic moments of 5 μ{sub B} are created by 3d{sup 5}({sup 6}S) states at each ionic core, which are coupled ferromagnetically to form molecular high-spin states via indirect exchange that is mediated in both cases by a delocalized valence electron in a singly occupied 4s derived antibonding molecular orbital with an unpaired spin. This leads to total magnetic moments of 11 μ{sub B} for Mn{sub 2}{sup +} and 16 μ{sub B} for Mn{sub 3}{sup +}, with no contribution of orbital angular momentum.

Discovery of novel compounds capable of electrochemical ion intercalation is a primary step toward development of advanced electrochemical devices such as batteries. Although cyano-bridged coordination polymers including Prussian blue analogues have been intensively investigated as ion intercalation materials, the solid-state electrochemistry of the octacyanotungstate-bridged coordination polymer has not been investigated. Here, we demonstrate that an octacyanotungstate-bridged coordination polymer Tb(H2O)5[W(CN)8] operates as a Li(+)-ion intercalation electrode material. The detailed magnetic measurements reveal that the tunable amount of intercalated Li(+) ion in the solid-state redox reaction between paramagnetic [W(V)(CN)8](3-) and diamagnetic [W(IV)(CN)8](4-) in the framework enables the electrochemical control of different magnetic regimes. While the initial ferromagnetic long-range ordering is irreversibly lost upon lithium insertion, electrochemical switching between paramagnetic and short-range ordering regimes can be achieved. PMID:27420412

The type II collagenopathies form a continuous spectrum of clinical severity, ranging from lethal achondrogenesis type II and hypochondrogenesis, through spondyloepiphyseal dysplasia, spondyloepimetaphyseal dysplasia and Kniest dysplasia to the Stickler syndrome and familial precocious osteoarthropathy at the mildest end of the spectrum. We have carried out a radiographic, morphologic, biochemical and molecular study in a case of achondrogenesis type II. Electron micrographs showed inclusion bodies of dilated rough endoplasmic reticulum in the chondrocytes and the presence of sparse collagen fibers in the cartilage matrix. Protein analysis of collagen from cartilage indicated posttranslational overmodification of the major cyanogen bromide peptides, and suggested a mutation near the carboxyl terminus of the type II collagen molecule. Analysis at the DNA level demonstrated that the phenotype was produced by a single base change (G-->C) that resulted in the substitution of glycine691 by arginine in the type II collagen triple helical domain. We confirm previous observations in three cases of hypochondrogenesis that glycine substitutions in the alpha 1(II) chain can result in a phenotype at the most severe end of the type II collagenopathy spectrum. PMID:7757081

Tetraspiro[2.1.2(5) .1.2(9) .1.2(13) .1(3) ]hexadecane-1,3,5,7-tetraone 4, a unique tetraketone containing a cyclooctane core and four spiroannelated cyclopropane moieties, represents the previously unknown cyclotetramer of carbonylcyclopropane. For this purpose oxidation of the parent polyspirocyclic hydrocarbon was examined under various oxidative conditions, and the reactivity of oxidants towards methylene groups of the eight-membered cycle, activated by adjacent spirocyclopropane rings, was evaluated and contrasted. Whereas the treatment of tetraspirohexadecane with ozone resulted in monooxidation, its reaction with methyl(trifluoromethyl)dioxirane afforded the product of four-fold oxidation, triketoalcohol 10. Subsequent oxidation of the latter with Dess-Martin periodinane gave the target tetraketone 4. PMID:26762227

The title compound, [Zr(3)(C(14)H(20)Si(2))(3)O(3)], consists of three disila-bridged zirconocene units, which are connected via an oxide ligand, forming a nearly planar six-membered ring with a maximum displacement of 0.0191 (8) Å. The compound was isolated as a by-product from a mixture of [(C(5)H(4)SiMe(2))(2)ZrCl(2)] and Li[AlH(4)] in Et(2)O. PMID:21753927

Prussian blue and its analogues have received particular attention as superior cathodes for Na-ion batteries due to their potential 2-Na storage capacity (∼170 mAh g(-1)) and low cost. However, most of the Prussian blue compounds obtained from the conventional synthetic routes contain large amounts of Fe(CN)6 vacancies and coordinated water molecules, which leads to the collapse of cyano-bridged framework and serious deterioration of their Na-storage ability. Herein, we propose a facile citrate-assisted controlled crystallization method to obtain low-defect Prussian blue lattice with greatly improved Na-storage capacity and cycling stability. As an example, the as-prepared Na2CoFe(CN)6 nanocrystals demonstrate a reversible 2-Na storage reaction with a high specific capacity of 150 mAh g(-1) and a ∼ 90% capacity retention over 200 cycles, possibly serving as a low cost and high performance cathode for Na-ion batteries. In particular, the synthetic strategy described in this work may be extended to other coordination-framework materials for a wide range of energy conversion and storage applications. PMID:26849278

By introducing large counter cations as the spacer, two isolated 3, 3-ladder compounds, (Ph4P)[CoII(3-Mepy)2.7(H2O)0.3WV(CN)8]·0.6H2O (1) and (Ph4As)[CoII(3-Mepy)3WV(CN)8] (2, 3-Mepy = 3-methylpyridine), were synthesized and characterized. Static and dynamic magnetic characterizations reveal that compounds 1 and 2 both behave as the single-chain magnets (SCMs) with very high energy barriers: 252(9) K for 1 and 224(7) K for 2, respectively. These two compounds display the highest relaxation barriers for cyano-bridged SCMs and are preceded only by two cobalt(II)-radical compounds among all SCMs. Meanwhile, a large coercive field of 26.2 kOe (1) and 22.6 kOe (2) were observed at 1.8 K.

Two new cyano-bridged two-dimensional heteronuclear complexes, [Cd(NH3)2(μ-ampy)Ni(μ-CN)2(CN)2]n (1) and [Cd(H2O)2(μ-ampy)Pt(μ-CN)2(CN)2]n (2) (ampy = 4-aminomethylpyridine), were synthesized and characterized by FT-IR and Raman spectroscopic, thermal (TG, DTG and DTA) and elemental analyses and single crystal X-ray diffraction techniques. They crystallize in the triclinic system and P-1 space group. The Ni(II) or Pt(II) ions are four coordinate with four cyanide-carbon atoms in a square planar geometry and the Cd(II) ion exhibits a distorted octahedral coordination by two different N-atoms from two symmetrically equivalent ampy ligands, two ammine or aqua ligands and two bridging cyano groups.The most important features of the complexes are the presence of obvious M&ctdot;π (M = Ni(II) or Pt(II)) interactions.

By introducing large counter cations as the spacer, two isolated 3, 3-ladder compounds, (Ph4P)[CoII(3-Mepy)2.7(H2O)0.3WV(CN)8]·0.6H2O (1) and (Ph4As)[CoII(3-Mepy)3WV(CN)8] (2, 3-Mepy = 3-methylpyridine), were synthesized and characterized. Static and dynamic magnetic characterizations reveal that compounds 1 and 2 both behave as the single-chain magnets (SCMs) with very high energy barriers: 252(9) K for 1 and 224(7) K for 2, respectively. These two compounds display the highest relaxation barriers for cyano-bridged SCMs and are preceded only by two cobalt(II)-radical compounds among all SCMs. Meanwhile, a large coercive field of 26.2 kOe (1) and 22.6 kOe (2) were observed at 1.8 K. PMID:27071451

By introducing large counter cations as the spacer, two isolated 3, 3-ladder compounds, (Ph4P)[Co(II)(3-Mepy)2.7(H2O)0.3W(V)(CN)8]·0.6H2O (1) and (Ph4As)[Co(II)(3-Mepy)3W(V)(CN)8] (2, 3-Mepy = 3-methylpyridine), were synthesized and characterized. Static and dynamic magnetic characterizations reveal that compounds 1 and 2 both behave as the single-chain magnets (SCMs) with very high energy barriers: 252(9) K for 1 and 224(7) K for 2, respectively. These two compounds display the highest relaxation barriers for cyano-bridged SCMs and are preceded only by two cobalt(II)-radical compounds among all SCMs. Meanwhile, a large coercive field of 26.2 kOe (1) and 22.6 kOe (2) were observed at 1.8 K. PMID:27071451

Influenza enters the host cell cytoplasm by fusing the viral and host membrane together. Fusion is mediated by hemagglutinin (HA) trimers that undergo conformational change when acidified in the endosome. It is currently debated how many HA trimers, w, and how many conformationally changed HA trimers, q, are minimally required for fusion. Conclusions vary because there are three common approaches for determining w and q from fusion data. One approach correlates the fusion rate with the fraction of fusogenic HA trimers and leads to the conclusion that one HA trimer is required for fusion. A second approach correlates the fusion rate with the total concentration of fusogenic HA trimers and indicates that more than one HA trimer is required. A third approach applies statistical models to fusion rate data obtained at a single HA density to establish w or q and suggests that more than one HA trimer is required. In this work, all three approaches are investigated through stochastic fusion simulations and experiments to elucidate the roles of HA and its ability to bend the target membrane during fusion. We find that the apparent discrepancies among the results from the various approaches may be resolved if nonfusogenic HA participates in fusion through interactions with a fusogenic HA. Our results, based on H3 and H1 serotypes, suggest that three adjacent HA trimers and one conformationally changed HA trimer are minimally required to induce membrane fusion (w = 3 and q = 1). PMID:24559987

In the context of HIV vaccine design and development, HIV-1 spike mimetics displaying a range of stabilities were evaluated to determine whether more stable, well-ordered trimers would more efficiently elicit neutralizing antibodies. To begin, in vitro analysis of trimers derived from the cysteine-stabilized SOSIP platform or the uncleaved, covalently linked NFL platform were evaluated. These native-like trimers, derived from HIV subtypes A, B, and C, displayed a range of thermostabilities, and were "stress-tested" at varying temperatures as a prelude to in vivo immunogenicity. Analysis was performed both in the absence and in the presence of two different adjuvants. Since partial trimer degradation was detected at 37°C before or after formulation with adjuvant, we sought to remedy such an undesirable outcome. Cross-linking (fixing) of the well-ordered trimers with glutaraldehyde increased overall thermostability, maintenance of well-ordered trimer integrity without or with adjuvant, and increased resistance to solid phase-associated trimer unfolding. Immunization of unfixed and fixed well-ordered trimers into animals revealed that the elicited tier 2 autologous neutralizing activity correlated with overall trimer thermostability, or melting temperature (Tm). Glutaraldehyde fixation also led to higher tier 2 autologous neutralization titers. These results link retention of trimer quaternary packing with elicitation of tier 2 autologous neutralizing activity, providing important insights for HIV-1 vaccine design. PMID:27487086

In the context of HIV vaccine design and development, HIV-1 spike mimetics displaying a range of stabilities were evaluated to determine whether more stable, well-ordered trimers would more efficiently elicit neutralizing antibodies. To begin, in vitro analysis of trimers derived from the cysteine-stabilized SOSIP platform or the uncleaved, covalently linked NFL platform were evaluated. These native-like trimers, derived from HIV subtypes A, B, and C, displayed a range of thermostabilities, and were “stress-tested” at varying temperatures as a prelude to in vivo immunogenicity. Analysis was performed both in the absence and in the presence of two different adjuvants. Since partial trimer degradation was detected at 37°C before or after formulation with adjuvant, we sought to remedy such an undesirable outcome. Cross-linking (fixing) of the well-ordered trimers with glutaraldehyde increased overall thermostability, maintenance of well-ordered trimer integrity without or with adjuvant, and increased resistance to solid phase-associated trimer unfolding. Immunization of unfixed and fixed well-ordered trimers into animals revealed that the elicited tier 2 autologous neutralizing activity correlated with overall trimer thermostability, or melting temperature (Tm). Glutaraldehyde fixation also led to higher tier 2 autologous neutralization titers. These results link retention of trimer quaternary packing with elicitation of tier 2 autologous neutralizing activity, providing important insights for HIV-1 vaccine design. PMID:27487086

We present an exploratory study that suggests that Efimov physics, a leading research theme in few-body quantum physics, can also induce stable many-body ground states whose building blocks are universal clusters. We identify a range of parameters in a mass-and-density-imbalanced two-species fermionic mixture for which the ground state is a gas of Efimov-related universal trimers. An explicit calculation of the trimer-trimer interaction reveals that the trimer phase is an SU(3) Fermi liquid stable against recombination losses. We propose to experimentally observe this phase in a fermionic 53Cr-6Li mixture.

Here, we quantitatively monitored and analyzed the spectral redistributions of the coupled plasmonic modes of trimeric Au nanostructures with two ∼1 nm interparticle gaps and single-dye-labeled DNA in each gap as a function of varying trimer symmetries. Our precise Mie scattering measurement with the laser-scanning-assisted dark-field microscopy allows for individual visualization of the orientations of the radiation fields of the coupled plasmon modes of the trimers and analyzing the magnitude and direction of the surface-enhanced Raman scattering (SERS) signals from the individual plasmonic trimers. We found that the geometric transition from acute-angled trimer to linear trimer induces the red shift of the longitudinally polarized mode and the blue shift of the axially polarized mode. The finite element method (FEM) calculation results show the distinct "on" and "off" of the plasmonic modes at the two gaps of the trimer. Importantly, the single-molecule-level systematic correlation studies among the near-field, far-field, and surface-enhanced Raman scattering reveal that the SERS signals from the trimers are determined by the largely excited coupled plasmon between the two competing plasmon modes, longitudinal and axial modes. Further, the FEM calculation revealed that even 0.5 nm or smaller discrepancy in the sizes of two gaps of the linear trimer led to >10-fold difference in the SERS signal. Granted that two gap sizes are not likely to be completely the same in actual experiments, one of two gaps plays a more significant role in generating the SERS signal. Overall, this work provides the knowledge and handles for the understanding and systematic control of the magnitude and polarization direction of the both plasmonic response and SERS signal from trimeric nanostructures and sets up the platform for the optical properties and the applications of plasmonically coupled trimers and higher multimeric nanostructures. PMID:26075353

The title compound, [Zr3(C14H20Si2)3O3], consists of three disila-bridged zirconocene units, which are connected via an oxide ligand, forming a nearly planar six-membered ring with a maximum displacement of 0.0191 (8) Å. The compound was isolated as a by-product from a mixture of [(C5H4SiMe2)2ZrCl2] and Li[AlH4] in Et2O. PMID:21753927

This article presents the first example of ultra-small (3-4 nm) magneto-luminescent cyano-bridged coordination polymer nanoparticles Ln0.333+Gdx3+/[Mo(CN)8]3- (Ln = Eu (x = 0.34), Tb (x = 0.35)) enwrapped by a natural biocompatible polymer chitosan. The aqueous colloidal solutions of these nanoparticles present a luminescence characteristic of the corresponding lanthanides (5D0 --> 7F0-4 (Eu3+) or the 5D4 --> 7F6-2 (Tb3+)) under UV excitation and a green luminescence of the chitosan shell under excitation in the visible region. Magnetic Resonance Imaging (MRI) efficiency, i.e. the nuclear relaxivity, measurements performed for Ln0.333+Gdx3+/[Mo(CN)8]3- nanoparticles show r1p and r2p relaxivities slightly higher than or comparable to the ones of the commercial paramagnetic compounds Gd-DTPA® or Omniscan® indicating that our samples may potentially be considered as a positive contrast agent for MRI. The in vitro studies performed on these nanoparticles show that they maybe internalized into human cancer and normal cells and well detected by fluorescence at the single cell level. They present high stability even at low pH and lack of cytotoxicity both in human cancer and normal cells.This article presents the first example of ultra-small (3-4 nm) magneto-luminescent cyano-bridged coordination polymer nanoparticles Ln0.333+Gdx3+/[Mo(CN)8]3- (Ln = Eu (x = 0.34), Tb (x = 0.35)) enwrapped by a natural biocompatible polymer chitosan. The aqueous colloidal solutions of these nanoparticles present a luminescence characteristic of the corresponding lanthanides (5D0 --> 7F0-4 (Eu3+) or the 5D4 --> 7F6-2 (Tb3+)) under UV excitation and a green luminescence of the chitosan shell under excitation in the visible region. Magnetic Resonance Imaging (MRI) efficiency, i.e. the nuclear relaxivity, measurements performed for Ln0.333+Gdx3+/[Mo(CN)8]3- nanoparticles show r1p and r2p relaxivities slightly higher than or comparable to the ones of the commercial paramagnetic compounds Gd

PowerPoint slide file that gives a brief history of the SAN Trimer contamination in Toms River, NJ as well as the EPA's provided technical support, specifically the development and application of the Provisional Peer-Reviewed Toxicity Value (PPRTV) assessment for SAN Trimer.

In vivo fluorescence microscopy and electron cryo-tomography have revealed that chemoreceptors self-assemble into extended honeycomb lattices of chemoreceptor trimers with a well-defined relative orientation of trimers. The signaling response of the observed chemoreceptor lattices is remarkable for its extreme sensitivity, which relies crucially on cooperative interactions among chemoreceptor trimers. In common with other membrane proteins, chemoreceptor trimers are expected to deform the surrounding lipid bilayer, inducing membrane-mediated anisotropic interactions between neighboring trimers. Here we introduce a biophysical model of bilayer-chemoreceptor interactions, which allows us to quantify the role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices. We find that, even in the absence of direct protein-protein interactions, membrane-mediated interactions can yield assembly of chemoreceptor lattices at very dilute trimer concentrations. The model correctly predicts the observed honeycomb architecture of chemoreceptor lattices as well as the observed relative orientation of chemoreceptor trimers, suggests a series of “gateway” states for chemoreceptor lattice assembly, and provides a simple mechanism for the localization of large chemoreceptor lattices to the cell poles. Our model of bilayer-chemoreceptor interactions also helps to explain the observed dependence of chemotactic signaling on lipid bilayer properties. Finally, we consider the possibility that membrane-mediated interactions might contribute to cooperativity among neighboring chemoreceptor trimers. PMID:25503274

Au-Au bond strengthening in photoexcited dimers of an Au(i) complex is captured in solution as oscillations of femtosecond absorption signals. The subsequent dynamics, when compared to the trimer's data, confirm that the bent-to-linear structural change of the trimer occurs in the first few picoseconds. PMID:26821585

Continuing investigations of multiphoton ionization processes in naphthalene have established the geometry and spectroscopy of trimer and tetramer cluster states. A new, highly efficient ionization mechanism has been identified in the trimer. It is closely related to autoionization of 2-electron atoms by resonant 2-photon excitation and to exciton fusion in larger clusters.

The highly conserved HIV-1 gp41 “pocket” region is a promising target for inhibiting viral entry. PIE12-trimer is a protease-resistant trimeric D-peptide inhibitor that binds to this pocket and potently blocks HIV entry. PIE12-trimer also possesses a reserve of binding energy that provides it with a strong genetic barrier to resistance (“resistance capacitor”). Here we report the design of a modular scaffold employing PEGs of discrete lengths for the efficient optimization and synthesis of PIE12-trimer. This scaffold also allows us to conjugate PIE12-trimer to several membrane-localizing cargoes, resulting in dramatically improved potency and retention of PIE12-trimer’s ability to absorb the impact of resistance mutations. This scaffold design strategy should be of broad utility for the rapid prototyping of multimeric peptide inhibitors attached to potency- or pharmacokinetic-enhancing groups. PMID:22545664

Ebolaviruses are highly lethal filoviruses that cause hemorrhagic fever in humans and nonhuman primates. With no approved treatments or preventatives, the development of an anti-ebolavirus therapy to protect against natural infections and potential weaponization is an urgent global health need. Here, we describe the design, biophysical characterization, and validation of peptide mimics of the ebolavirus N-trimer, a highly conserved region of the GP2 fusion protein, to be used as targets to develop broad-spectrum inhibitors of ebolavirus entry. The N-trimer region of GP2 is 90% identical across all ebolavirus species and forms a critical part of the prehairpin intermediate that is exposed during viral entry. Specifically, we fused designed coiled coils to the N-trimer to present it as a soluble trimeric coiled coil as it appears during membrane fusion. Circular dichroism, sedimentation equilibrium, and X-ray crystallography analyses reveal the helical, trimeric structure of the designed N-trimer mimic targets. Surface plasmon resonance studies validate that the N-trimer mimic binds its native ligand, the C-peptide region of GP2. The longest N-trimer mimic also inhibits virus entry, thereby confirming binding of the C-peptide region during viral entry and the presence of a vulnerable prehairpin intermediate. Using phage display as a model system, we validate the suitability of the N-trimer mimics as drug screening targets. Finally, we describe the foundational work to use the N-trimer mimics as targets in mirror-image phage display, which will be used to identify d-peptide inhibitors of ebolavirus entry. PMID:25287718

Ebolaviruses are highly lethal filoviruses that cause hemorrhagic fever in humans and nonhuman primates. With no approved treatments or preventatives, the development of an anti-ebolavirus therapy to protect against natural infections and potential weaponization is an urgent global health need. Here, we describe the design, biophysical characterization, and validation of peptide mimics of the ebolavirus N-trimer, a highly conserved region of the GP2 fusion protein, to be used as targets to develop broad-spectrum inhibitors of ebolavirus entry. The N-trimer region of GP2 is 90% identical across all ebolavirus species and forms a critical part of the prehairpin intermediate that is exposed during viral entry. Specifically, we fused designed coiled coils to the N-trimer to present it as a soluble trimeric coiled coil as it appears during membrane fusion. Circular dichroism, sedimentation equilibrium, and X-ray crystallography analyses reveal the helical, trimeric structure of the designed N-trimer mimic targets. Surface plasmon resonance studies validate that the N-trimer mimic binds its native ligand, the C-peptide region of GP2. The longest N-trimer mimic also inhibits virus entry, thereby confirming binding of the C-peptide region during viral entry and the presence of a vulnerable prehairpin intermediate. Using phage display as a model system, we validate the suitability of the N-trimer mimics as drug screening targets. Finally, we describe the foundational work to use the N-trimer mimics as targets in mirror-image phage display, which will be used to identify D-peptide inhibitors of ebolavirus entry. PMID:25287718

The severe acute respiratory syndrome coronavirus enters cells through the activities of a spike protein (S) which has receptor-binding (S1) and membrane fusion (S2) regions. We have characterized four sequential states of a purified recombinant S ectodomain (S-e) comprising S1 and the ectodomain of S2. They are S-e monomers, uncleaved S-e trimers, cleaved S-e trimers, and dissociated S1 monomers and S2 trimer rosettes. Lowered pH induces an irreversible transition from flexible, L-shaped S-e monomers to clove-shaped trimers. Protease cleavage of the trimer occurs at the S1-S2 boundary; an ensuing S1 dissociation leads to a major rearrangement of the trimeric S2 and to formation of rosettes likely to represent clusters of elongated, postfusion trimers of S2 associated through their fusion peptides. The states and transitions of S suggest conformational changes that mediate viral entry into cells. PMID:16809285

Semliki Forest virus (SFV) is an enveloped alphavirus that infects cells by a low-pH-triggered membrane fusion reaction mediated by the viral E1 protein. E1 inserts into target membranes and refolds to a hairpin-like homotrimer containing a central core trimer and an outer layer composed of domain III and the juxtamembrane stem region. The key residues involved in mediating E1 trimerization are not well understood. We recently showed that aspartate 188 in the interface of the core trimer plays a critical role. Substitution with lysine (D188K) blocks formation of the core trimer and E1 trimerization and strongly inhibits virus fusion and infection. Here, we have isolated and characterized revertants that rescued the fusion and growth defects of D188K. These revertants included pseudorevertants containing acidic or polar neutral residues at E1 position 188 and a second-site revertant containing an E1 K176T mutation. Computational analysis using multiconformation continuum electrostatics revealed an important interaction bridging D188 of one chain with K176 of the adjacent chain in the core trimer. E1 K176 is completely conserved among the alphaviruses, and mutations of K176 to threonine (K176T) or isoleucine (K176I) produced similar fusion phenotypes as D188 mutants. Together, our data support a model in which a ring of three salt bridges formed by D188 and K176 stabilize the core trimer, a key intermediate of the alphavirus fusion protein. PMID:20826687

Seed protein proglobulins were synthesized from cDNAs in reticulocyte lysates. Most proglobulins were recovered as trimers when translation rates were low, but mostly monomers were recovered at high translation rates. The prevalence of monomers was accompanied by elevated amounts of insoluble protein recovered at the bottom of sucrose density gradients. Apyrase treatment of translation mixtures after synthesis, but before significant assembly occurred, drastically reduced trimer assembly and increased the proportion of insoluble aggregate. These observations indicated that ATP is required for protein folding and/or trimer assembly. The appearance of insoluble aggregated protein when rates of synthesis were elevated or when ATP was absent suggested that protein misfolding had occurred. Trimer assembly was stimulated when wheat germ translation mixtures defective in supporting efficient trimer assembly were supplemented with fractions isolated from endoplasmic reticula of developing pea (Pisum sativum) seeds. Molecular chaperones are likely involved in folding and/or assembly of proglobulin trimers both in reticulocyte lysates and in seeds. Consistent with this hypothesis, trimer formation was reduced when carboxymethylated bovine albumin and alpha-casein, considered to mimic proteins with extended chain and molten globular conformations and thereby compete for Hsp70- and Hsp60-type molecular chaperones, respectively, were introduced into translation mixtures. PMID:9414566

Mixtures of polarized fermions of two different masses can form weakly bound clusters, such as dimers and trimers, that are universally described by the scattering length between the heavy and light fermions. We use the resonating group method to investigate the low-energy scattering processes involving dimers or trimers. The method reproduces approximately the known particle–dimer and dimer–dimer scattering lengths. We use it to estimate the trimer–trimer scattering length, which is presently unknown, and find it to be positive.

Shallow heteronuclear trimers are predicted for mixtures of two atomic species strongly trapped in a quasi-two-dimensional (2D) atomic waveguide. The binding energies are functions of the 2D scattering length and of the mass ratio and can be thus tuned by various ways. These universal trimers are composed of two identical noninteracting particles and of a third particle of the other species. Depending on the statistics of the two identical particles, the trimers have an odd (fermions) or even (bosons) internal angular momentum. These results permit one to draw conclusions on the stability issue for the quasi-2D gaseous phase of heteronuclear dimers.

The quantum-degenerate unitary Bose gas has been studied in an experiment at JILA in which a Bose-Einstein condensate was quickly ramped to infinite scattering length. The sudden approximation can be used to calculate the probability for creating Efimov trimers. A trimer that is created in a region of the BEC where its decay rate is faster than its reaction rate from atom-trimer scattering can contribute to the initial atom loss rate. We use universal 3-body and 4-body results to estimate the initial atom loss rate. This work was supported in part by the National Science Foundation.

Carboxylated schizophyllan (sclerox) samples of different degrees of oxidation were molecularly characterized by size exclusion chromatography equipped with a multi-angle light scattering detector (SEC-MALS) in 0.10 M aqueous NaCl solution. The molar mass distribution obtained by SEC-MALS shows that sclerox of low degree of oxidation is dissolved mainly as the trimer, whereas the trimer and single chain coexist in solution of sclerox of high degree of oxidation. The trimer of sclerox is much more flexible than the fully ordered triple helix of the parent schizophyllan and easily dissociates into single chains upon heating. PMID:26428092

3-phenyl-propynenitrile (PPN) adsorbs on Cu(111) in a hexagonal network of molecular trimers formed through intermolecular interaction of the cyano group of one molecule with the aromatic ring of its neighbor. Heptamers of trimers coalesce into interlocking pinwheel-shaped structures that, by percolating across islands of the original trimer coverage, create the appearance of gear chains. Density functional theory aids in identifying substrate stress associated with the chemisorption of PPN's acetylene group as the cause of this transition. PMID:21992333

We have engineered a metal-binding site into the novel artificial β-propeller protein Pizza. This new Pizza variant carries two nearly identical domains per polypeptide chain, and forms a trimer with three-fold symmetry. The designed single metal ion binding site lies on the symmetry axis, bonding the trimer together. Two copies of the trimer associate in the presence of cadmium chloride in solution, and very high-resolution X-ray crystallographic analysis reveals a nanocrystal of cadmium chloride, sandwiched between two trimers of the protein. This nanocrystal, containing seven cadmium ions lying in a plane and twelve interspersed chloride ions, is the smallest reported to date. Our results indicate the feasibility of using rationally designed symmetrical proteins to biomineralize nanocrystals with useful properties. PMID:26136355

New type of trifunctional alcohol was synthesized from commercially available trimer acid. Trifunctional alcohol is hydrocarbon with widely separated terminal hydroxyl groups, and was expressly developed as crosslinking agent for preparation of polyurethane propellants, binders and case liners.

The heat shock response is a universal homeostatic cell autonomous reaction of organisms to cope with adverse environmental conditions. In mammalian cells, this response is mediated by the heat shock transcription factor Hsf1, which is monomeric in unstressed cells and upon activation trimerizes, and binds to promoters of heat shock genes. To understand the basic principle of Hsf1 activation we analyzed temperature-induced alterations in the conformational dynamics of Hsf1 by hydrogen exchange mass spectrometry. We found a temperature-dependent unfolding of Hsf1 in the regulatory region happening concomitant to tighter packing in the trimerization region. The transition to the active DNA binding-competent state occurred highly cooperative and was concentration dependent. Surprisingly, Hsp90, known to inhibit Hsf1 activation, lowered the midpoint temperature of trimerization and reduced cooperativity of the process thus widening the response window. Based on our data we propose a kinetic model of Hsf1 trimerization. PMID:26785146

Mechanisms for the appearance of disorder on the As-rich GaAs(111)A surface were investigated employing density functional theory (DFT). Focus was given to the As trimer interactions by considering different surface symmetries and rest site occupations. The (2 × 2) and the c(4 × 2) structure models with As trimer and an As rest site were found the most energetically stable under the As-rich experimental conditions at T = 0 K. Low interactions between neighboring As trimers causes disorder in thermodynamic equilibrium at finite temperatures. A careful analysis of the configurational entropy contributions including the different statistics was carried out. The experimentally observed As-rich (2 × 2) structure was confirmed to be kinetically stabilized. The stabilization mechanism is discussed with respect to the As trimer migration on the surface, which is limited by a large diffusion barrier through the As rest sites.

A p-cresol trimer sequence was incorporated into a polymeric chain of novolak by copolymerization with m-cresol of a reactive precursor which was prepared by attaching two units of m-cresol to the terminal ortho positions of p-cresol trimer. The resulting novolak was characterized by 13C NMR and FTIR in an attempt to correlate novolak structure with dissolution inhibition function based on physicochemical analysis of molecular interactions between novolak and DNQ-PAC in solid films.

ABSTRACT The noncovalent interactions that mediate trimerization of the influenza hemagglutinin (HA) are important determinants of its biological activities. Recent studies have demonstrated that mutations in the HA trimer interface affect the thermal and pH sensitivities of HA, suggesting a possible impact on vaccine stability (). We used size exclusion chromatography analysis of recombinant HA ectodomain to compare the differences among recombinant trimeric HA proteins from early 2009 pandemic H1N1 viruses, which dissociate to monomers, with those of more recent virus HAs that can be expressed as trimers. We analyzed differences among the HA sequences and identified intermolecular interactions mediated by the residue at position 374 (HA0 numbering) of the HA2 subdomain as critical for HA trimer stability. Crystallographic analyses of HA from the recent H1N1 virus A/Washington/5/2011 highlight the structural basis for this observed phenotype. It remains to be seen whether more recent viruses with this mutation will yield more stable vaccines in the future. IMPORTANCE Hemagglutinins from the early 2009 H1N1 pandemic viruses are unable to maintain a trimeric complex when expressed in a recombinant system. However, HAs from 2010 and 2011 strains are more stable, and our work highlights that the improvement in stability can be attributed to an E374K substitution in the HA2 subunit of the stalk that emerged naturally in the circulating viruses. PMID:24522930

Part I. The work presented herein describes efforts to develop general techniques for the synthesis of transition metal clusters and the manipulation of their properties. In Chapter 2, it is demonstrated that a modified metal atom reactor allows for the vaporization, passivation, and isolation of metal-chalcogenide clusters from their parent binary solids. Among the clusters produced by this method were Cr6S8(PEt3)6, Fe4S 4(PEt3)4, Co6S8(PEt 3)6, Cu6S4(PEt3)6, Cu12S6(PEt3)8, and Cu26Se 13(PEt3)14. To create single-molecule magnets with higher demagnetization barriers, we are developing metal-cyanide systems which exhibit highly adjustable magnetic behavior. Chapter 3 reports an attempt to introduce magnetic anisotropy into a MnCr6 cluster. Replacement of CrIII with Mo III resulted in the assembly of K[(Me3tacn)6MnMo 6(CN)18](ClO4)3 (Me3tacn = N,N',N″ -trimethyl-1,4,7-triazacyclononane)---the first well-documented example of a cyano-bridged single-molecule magnet. Recently, it was demonstrated that replacing Me3tacn with the less sterically hindering tach (tach = cis,cis-1,3,5-triaminocyclohexane) in the face-centered cubic cluster [(tach)8Cr8Ni 6(CN)24]Br12 provides greater access to the cluster cavity. Chapter 4 describes my efforts to probe the selectivity of this cluster toward inclusion of various guests. Part II. Successful implementation of student-centered curricula reforms requires the creation of a measurement instrument for monitoring whether the curricula are being used as intended. The creation and development of an observation instrument would greatly contribute to this effort. To develop a theoretically sound construct map, it is necessary to review the literature and conduct our own investigations of approaches to science teaching. Chapter 2 presents the findings of these investigations and their contributions to our understanding of the construct. Using these findings, the Science Teaching Observation Protocol (STOP) was created and designed to

Eliciting broad tier 2 neutralizing antibodies (nAbs) is a major goal of HIV-1 vaccine research. Here we investigated the ability of native, membrane-expressed JR-FL Env trimers to elicit nAbs. Unusually potent nAb titers developed in 2 of 8 rabbits immunized with virus-like particles (VLPs) expressing trimers (trimer VLP sera) and in 1 of 20 rabbits immunized with DNA expressing native Env trimer, followed by a protein boost (DNA trimer sera). All 3 sera neutralized via quaternary epitopes and exploited natural gaps in the glycan defenses of the second conserved region of JR-FL gp120. Specifically, trimer VLP sera took advantage of the unusual absence of a glycan at residue 197 (present in 98.7% of Envs). Intriguingly, removing the N197 glycan (with no loss of tier 2 phenotype) rendered 50% or 16.7% (n = 18) of clade B tier 2 isolates sensitive to the two trimer VLP sera, showing broad neutralization via the surface masked by the N197 glycan. Neutralizing sera targeted epitopes that overlap with the CD4 binding site, consistent with the role of the N197 glycan in a putative “glycan fence” that limits access to this region. A bioinformatics analysis suggested shared features of one of the trimer VLP sera and monoclonal antibody PG9, consistent with its trimer-dependency. The neutralizing DNA trimer serum took advantage of the absence of a glycan at residue 230, also proximal to the CD4 binding site and suggesting an epitope similar to that of monoclonal antibody 8ANC195, albeit lacking tier 2 breadth. Taken together, our data show for the first time that strain-specific holes in the glycan fence can allow the development of tier 2 neutralizing antibodies to native spikes. Moreover, cross-neutralization can occur in the absence of protecting glycan. Overall, our observations provide new insights that may inform the future development of a neutralizing antibody vaccine. PMID:26023780

Recombinant subunit vaccines should contain minimal non-pathogen motifs to reduce potential off-target reactivity. We recently developed a vaccine antigen against respiratory syncytial virus (RSV), which comprised the fusion (F) glycoprotein stabilized in its pre-fusion trimeric conformation by “DS-Cav1” mutations and by an appended C-terminal trimerization motif or “foldon” from T4-bacteriophage fibritin. Here we investigate the creation of a cysteine zipper to allow for the removal of the phage foldon, while maintaining the immunogenicity of the parent DS-Cav1+foldon antigen. Constructs without foldon yielded RSV F monomers, and enzymatic removal of the phage foldon from pre-fusion F trimers resulted in their dissociation into monomers. Because the native C terminus of the pre-fusion RSV F ectodom